Editing Folding@home

{{short description|Distributed computing project simulating protein folding}}
{{Use American English|date=August 2021}}
{{Infobox software
| name = Folding@home
| logo = FAH Logo.svg
| logo_size = 200px
| author = Vijay Pande
| developer = Pande Laboratory, [[Sony]], [[Nvidia]], [[ATI Technologies]], Joseph Coffland, Cauldron Development<ref name="About Partners"/>
| released = {{Start date and age|2000|10|01}}
| latest release version = 8.4.9
| latest release date = {{Start date and age|2024|11|20}}<ref name="Public client releases"/>
| operating system = [[Microsoft Windows]], [[macOS]], [[Linux]], [[PlayStation 3]] (discontinued as of firmware version 4.30)
| platform = [[IA-32]], [[x86-64]], [[ARM64]], [[CUDA]]<ref>{{cite web | url=https://foldingathome.org/alternative-downloads/?lng=en | title=Alternative Downloads }}</ref>
| language = English, French, Spanish, Swedish
| genre = [[Distributed computing]]
| license = Proprietary software (before version 8)<ref name="Open Source FAQ"/><br>[[GPL-3.0-or-later]] (version 8)
| website = {{official URL}}
}}

'''Folding@home''' ('''FAH''' or '''F@h''') is a [[distributed computing]] project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating [[protein dynamics]]. This includes the process of [[protein folding]] and the movements of [[protein]]s, and is reliant on simulations run on volunteers' [[personal computer]]s.<ref>{{harvnb|Folding@home|n.d.e}}: "Folding@home (FAH or F@h) is a distributed computing project for simulating protein dynamics, including the process of protein folding and the movements of proteins implicated in a variety of diseases. It brings together citizen scientists who volunteer to run simulations of protein dynamics on their personal computers. Insights from this data are helping scientists to better understand biology, and providing new opportunities for developing therapeutics."</ref> Folding@home is currently based at the [[University of Pennsylvania]] and led by [[Greg Bowman]], a former student of [[Vijay S. Pande|Vijay Pande]].<ref name="FAH leadership change"/>

The project utilizes [[graphics processing unit]]s (GPUs), [[central processing unit]]s (CPUs), and [[ARM architecture|ARM]] processors like those on the [[Raspberry Pi]] for distributed computing and scientific research. The project uses statistical [[simulation]] methodology that is a [[paradigm shift]] from traditional computing methods.<ref name="10.1016/j.ymeth.2010.06.002"/> As part of the [[client–server model]] [[network architecture]], the volunteered machines each receive pieces of a simulation (work units), complete them, and return them to the project's [[database server]]s, where the units are compiled into an overall simulation. Volunteers can track their contributions on the Folding@home website, which makes volunteers' participation competitive and encourages long-term involvement.

Folding@home is one of the world's fastest computing systems. With heightened interest in the project as a result of the [[COVID-19 pandemic]],<ref>{{harvnb|News 12 Staff|2020}}: "Since the start of the COVID-19 pandemic, Folding@home has seen a significant surge in downloads, a clear indication that people around the world are concerned about doing their part to help researchers find a remedy to this virus," said Dr. Sina Rabbany, dean of the DeMatteis School."</ref> the system achieved a speed of approximately 1.22 [[FLOPS|exaflops]] by late March 2020 and reached 2.43 exaflops by April 12, 2020,<ref>{{cite web | url = https://stats.foldingathome.org/os | archive-url = https://archive.today/20200412111010/https://stats.foldingathome.org/os | url-status = dead | archive-date = April 12, 2020 | title = Client Statistics by OS | author = Pande lab | publisher = Archive.is | access-date = April 12, 2020}}</ref> making it the world's first [[Exascale computing|exaflop computing system]]. This level of performance from its large-scale computing network has allowed researchers to run [[Analysis of algorithms|computationally costly]] atomic-level simulations of protein folding thousands of times longer than formerly achieved. Since its launch on October&nbsp;1, 2000, Folding@home has been involved in the production of 226 [[Academic publishing|scientific research papers]].<ref name="papers-july-2020">{{cite web |title=Papers & Results |url=https://foldingathome.org/papers-results/ |website=Folding@home.org |access-date=December 9, 2021}}</ref> Results from the project's simulations agree well with experiments.<ref name="10.1021/ja9090353"/><ref name="10.1073/pnas.1003962107"/><ref name="10.1038/nature01160"/>

== Background ==
{{further|Protein folding}}
[[File:Protein folding.png|thumb|A protein before and after folding. It starts in an unstable [[random coil]] state and finishes in its native state conformation.]]

[[Protein]]s are an essential component to many biological functions and participate in virtually all processes within [[Cell (biology)|biological cell]]s. They often act as [[enzyme]]s, performing biochemical reactions including [[cell signaling]], molecular transportation, and [[Cell cycle#Regulation of eukaryotic cell cycle|cellular regulation]]. As structural elements, some proteins act as a type of [[cytoskeleton|skeleton for cells]], and as [[antibodies]], while other proteins participate in the [[immune system]]. Before a protein can take on these roles, it must fold into a functional [[Protein tertiary structure|three-dimensional structure]], a process that often occurs spontaneously and is dependent on interactions within its [[amino acid]] sequence and interactions of the amino acids with their surroundings. Protein folding is driven by the search to find the most energetically favorable conformation of the protein, i.e., its [[native state]]. Thus, understanding protein folding is critical to understanding what a protein does and how it works, and is considered a holy grail of [[computational biology]].<ref name="10.1371/journal.pcbi.1000452"/><ref name="10.1126/science.309.5731.78b"/> Despite folding occurring within a [[macromolecular crowding|crowded cellular environment]], it typically proceeds smoothly. However, due to a protein's chemical properties or other factors, proteins may [[protein misfolding|misfold]], that is, fold down the wrong pathway and end up misshapen. Unless cellular mechanisms can destroy or refold misfolded proteins, they can subsequently [[Protein aggregation|aggregate]] and cause a variety of debilitating diseases.<ref name="10.1002/iub.117"/> Laboratory experiments studying these processes can be limited in scope and atomic detail, leading scientists to use physics-based computing models that, when complementing experiments, seek to provide a more complete picture of protein folding, misfolding, and aggregation.<ref name="10.1016/j.abb.2007.05.014"/><ref name="10.1016/j.cbpa.2008.02.011"/>

Due to the complexity of proteins' conformation or [[Configuration space (physics)|configuration space]] (the set of possible shapes a protein can take), and limits in computing power, all-atom molecular dynamics simulations have been severely limited in the timescales that they can study. While most proteins typically fold in the order of milliseconds,<ref name="10.1016/j.abb.2007.05.014"/><ref name="10.1146/annurev.biophys.34.040204.144447"/> before 2010, simulations could only reach nanosecond to microsecond timescales.<ref name="10.1021/ja9090353"/> General-purpose [[supercomputer]]s have been used to simulate protein folding, but such systems are intrinsically costly and typically shared among many research groups. Further, because the computations in kinetic models occur serially, strong [[scalability|scaling]] of traditional molecular simulations to these architectures is exceptionally difficult.<ref name="978-1-58603-796-3"/><ref name="10.1002/bip.10219"/> Moreover, as protein folding is a [[stochastic process]] (i.e., random) and can statistically vary over time, it is challenging computationally to use long simulations for comprehensive views of the folding process.<ref name="10.1016/j.sbi.2010.10.006"/><ref name="10.1137/06065146X"/>

[[File:ACBP MSM from Folding@home.tiff|thumb|Folding@home uses [[Markov state model]]s, like the one diagrammed here, to model the possible shapes and folding pathways a protein can take as it condenses from its initial randomly coiled state (left) into its native 3-D structure (right).]]
Protein folding does not occur in one step.<ref name="10.1002/iub.117"/> Instead, proteins spend most of their folding time, nearly 96% in some cases,<ref name="10.1016/j.sbi.2011.12.001"/> ''waiting'' in various intermediate [[protein conformation|conformational]] states, each a local [[thermodynamic free energy]] minimum in the protein's [[energy landscape]]. Through a process known as [[adaptive sampling]], these conformations are used by Folding@home as starting points for a [[set (mathematics)|set]] of simulation trajectories. As the simulations discover more conformations, the trajectories are restarted from them, and a [[Hidden Markov model|Markov state model]] (MSM) is gradually created from this cyclic process. MSMs are [[discrete-time]] [[master equation]] models which describe a biomolecule's conformational and energy landscape as a set of distinct structures and the short transitions between them. The adaptive sampling Markov state model method significantly increases the efficiency of simulation as it avoids computation inside the local energy minimum itself, and is amenable to distributed computing (including on [[GPUGRID]]) as it allows for the statistical aggregation of short, independent simulation trajectories.<ref name="Simulation FAQ"/> The amount of time it takes to construct a Markov state model is inversely proportional to the number of parallel simulations run, i.e., the number of processors available. In other words, it achieves linear [[parallelization]], leading to an approximately four [[orders of magnitude]] reduction in overall serial calculation time. A completed MSM may contain tens of thousands of sample states from the protein's [[phase space]] (all the conformations a protein can take on) and the transitions between them. The model illustrates folding events and pathways (i.e., routes) and researchers can later use kinetic clustering to view a coarse-grained representation of the otherwise highly detailed model. They can use these MSMs to reveal how proteins misfold and to quantitatively compare simulations with experiments.<ref name="10.1016/j.ymeth.2010.06.002"/><ref name="10.1016/j.sbi.2010.10.006"/><ref name="10.1021/ct900620b"/>

Between 2000 and 2010, the length of the proteins Folding@home has studied have increased by a factor of four, while its timescales for protein folding simulations have increased by six orders of magnitude.<ref name="typepad: how far FAH has come"/> In 2002, Folding@home used Markov state models to complete approximately a million [[CPU]] days of simulations over the span of several months,<ref name="10.1038/nature01160"/> and in 2011, MSMs parallelized another simulation that required an aggregate 10&nbsp;million CPU hours of computing.<ref name="10.1073/pnas.1010880108"/> In January 2010, Folding@home used MSMs to simulate the dynamics of the slow-folding 32-[[amino acid|residue]] NTL9 protein out to 1.52&nbsp;milliseconds, a timescale consistent with experimental folding rate predictions but a thousand times longer than formerly achieved. The model consisted of many individual trajectories, each two orders of magnitude shorter, and provided an unprecedented level of detail into the protein's energy landscape.<ref name="10.1016/j.ymeth.2010.06.002"/><ref name="10.1021/ja9090353"/><ref name="10.3390/ijms11125292"/> In 2010, Folding@home researcher Gregory Bowman was awarded the [[Thomas Kuhn#Thomas Kuhn Paradigm Shift Award|Thomas Kuhn Paradigm Shift Award]] from the [[American Chemical Society]] for the development of the [[open-source software|open-source]] MSMBuilder software and for attaining quantitative agreement between theory and experiment.<ref name="2010 KPS award"/><ref name="MSMBuilder source"/> For his work, Pande was awarded the 2012 Michael and Kate Bárány Award for Young Investigators for "developing field-defining and field-changing computational methods to produce leading theoretical models for protein and [[RNA]] folding",<ref name="Biophysical society names recipients"/> and the 2006 Irving Sigal Young Investigator Award for his simulation results which "have stimulated a re-examination of the meaning of both ensemble and single-molecule measurements, making Pande's efforts pioneering contributions to simulation methodology."<ref name="FAH Awards"/>

== Examples of application in biomedical research ==
Protein misfolding can result in a [[proteopathy|variety of diseases]] including Alzheimer's disease, [[cancer]], [[Creutzfeldt–Jakob disease]], [[cystic fibrosis]], Huntington's disease, [[sickle-cell anemia]], and [[type&nbsp;II diabetes]].<ref name="10.1002/iub.117"/><ref name="Protein Misfolding Diseases"/><ref name="diseases FAQ"/> Cellular infection by viruses such as [[HIV]] and [[influenza]] also involve folding events on [[cell membrane]]s.<ref name="978-0-340-66316-5"/> Once protein misfolding is better understood, therapies can be developed that augment cells' natural ability to regulate protein folding. Such [[therapies]] include the use of engineered molecules to alter the production of a given protein, help destroy a misfolded protein, or assist in the folding process.<ref name="10.1038/nature02265"/> The combination of computational molecular modeling and experimental analysis has the possibility to fundamentally shape the future of molecular medicine and the [[drug design|rational design of therapeutics]],<ref name="10.1016/j.cbpa.2008.02.011"/> such as expediting and lowering the costs of [[drug discovery]].<ref name="10.1093/bib/bbp023"/> The goal of the first five years of Folding@home was to make advances in understanding folding, while the current goal is to understand misfolding and related disease, especially Alzheimer's.<ref name="Press FAQ"/>

The simulations run on Folding@home are used in conjunction with laboratory experiments,<ref name="10.1016/j.sbi.2010.10.006"/> but researchers can use them to study how folding ''[[in vitro]]'' differs from folding in native cellular environments. This is advantageous in studying aspects of folding, misfolding, and their relationships to disease that are difficult to observe experimentally. For example, in 2011, Folding@home simulated protein folding inside a [[ribosome|ribosomal]] exit tunnel, to help scientists better understand how natural confinement and crowding might influence the folding process.<ref name="forum: 7808/7809 to FAH"/><ref name="10.1073/pnas.0608256104"/> Furthermore, scientists typically employ chemical [[denaturation (biochemistry)|denaturants]] to unfold proteins from their stable native state. It is not generally known how the denaturant affects the protein's refolding, and it is difficult to experimentally determine if these denatured states contain residual structures which may influence folding behavior. In 2010, Folding@home used GPUs to simulate the unfolded states of [[Protein&nbsp;L]], and predicted its collapse rate in strong agreement with experimental results.<ref name="10.1021/ja908369h"/>

The large data sets from the project are freely available for other researchers to use upon request and some can be accessed from the Folding@home website.<ref name="typepad: Simbios"/><ref name="papers for free"/> The Pande lab has collaborated with other molecular dynamics systems such as the [[Blue Gene]] supercomputer,<ref name="10.1038/sj.embor.7400108"/> and they share Folding@home's key software with other researchers, so that the algorithms which benefited Folding@home may aid other scientific areas.<ref name="typepad: Simbios"/> In 2011, they released the open-source Copernicus software, which is based on Folding@home's MSM and other parallelizing methods and aims to improve the efficiency and scaling of molecular simulations on large [[computer cluster]]s or [[supercomputer]]s.<ref name="Pronk et al, 2011" /><ref name="Copernicus download"/> Summaries of all scientific findings from Folding@home are posted on the Folding@home website after publication.<ref name="papers"/>

=== Alzheimer's disease ===
{{Multiple image|footer= Alzheimer's disease is linked to the aggregation of amyloid beta protein fragments in the brain (right). Researchers have used Folding@home to simulate this aggregation process, to better understand the cause of the disease.|image1= Amyloid 01big1.jpg|image2= Amyloid 02big1.jpg|image3= Amyloid 03big1.jpg}}

[[Alzheimer's disease]] is an incurable [[neurodegeneration|neurodegenerative]] disease which most often affects the elderly and accounts for more than half of all cases of [[dementia]]. Its exact cause remains unknown, but the disease is identified as a [[proteopathy|protein misfolding disease]]. Alzheimer's is associated with toxic [[protein aggregation|aggregations]] of the [[amyloid beta]] (Aβ) [[peptide]], caused by Aβ misfolding and clumping together with other Aβ peptides. These Aβ aggregates then grow into significantly larger [[senile plaques]], a pathological marker of Alzheimer's disease.<ref name="10.2119/2007-00100.Irvine"/><ref name="10.1001/archneurol.2007.56"/><ref name="10.1074/jbc.R800036200"/> Due to the heterogeneous nature of these aggregates, experimental methods such as [[X-ray crystallography]] and [[nuclear magnetic resonance]] (NMR) have had difficulty characterizing their structures. Moreover, atomic simulations of Aβ aggregation are highly demanding computationally due to their size and complexity.<ref name="10.1063/1.3010881"/><ref name="10.1371/journal.pone.0021776"/>

Preventing Aβ aggregation is a promising method to developing therapeutic drugs for Alzheimer's disease, according to Naeem and Fazili in a [[literature review]] article.<ref name="10.1007/s12013-011-9200-x"/> In 2008, Folding@home simulated the dynamics of Aβ aggregation in atomic detail over timescales of the order of tens of seconds. Prior studies were only able to simulate about 10 microseconds. Folding@home was able to simulate Aβ folding for six orders of magnitude longer than formerly possible. Researchers used the results of this study to identify a [[beta hairpin]] that was a major source of molecular interactions within the structure.<ref name="10.1038/cr.2010.57"/> The study helped prepare the Pande lab for future aggregation studies and for further research to find a small peptide which may stabilize the aggregation process.<ref name="10.1063/1.3010881"/>

In December 2008, Folding@home found several small drug candidates which appear to inhibit the toxicity of Aβ aggregates.<ref name="typepad: possible alz. drug"/> In 2010, in close cooperation with the Center for Protein Folding Machinery, these drug leads began to be tested on [[biological tissue]].<ref name="diseases FAQ"/> In 2011, Folding@home completed simulations of several [[mutation]]s of Aβ that appear to stabilize the aggregate formation, which could aid in the development of therapeutic drug therapies for the disease and greatly assist with experimental [[nuclear magnetic resonance spectroscopy]] studies of Aβ [[oligomer]]s.<ref name="10.1371/journal.pone.0021776"/><ref name="10.1021/jm201332p"/> Later that year, Folding@home began simulations of various Aβ fragments to determine how various natural enzymes affect the structure and folding of Aβ.<ref name="forum: 6871"/><ref name="description: 6571"/>

=== Huntington's disease ===
[[Huntington's disease]] is a neurodegenerative [[genetic disorder]] that is associated with protein misfolding and aggregation. [[Polyglutamine tract|Excessive repeats]] of the [[glutamine]] amino acid at the [[N-terminus]] of the [[huntingtin protein]] cause aggregation, and although the behavior of the repeats is not completely understood, it does lead to the cognitive decline associated with the disease.<ref name="10.1016/S0140-6736(07)60111-1"/> As with other aggregates, there is difficulty in experimentally determining its structure.<ref name="10.1016/j.jmb.2009.01.032"/> Scientists are using Folding@home to study the structure of the huntingtin protein aggregate and to predict how it forms, assisting with [[rational drug design]] methods to stop the aggregate formation.<ref name="diseases FAQ"/> The N17 fragment of the huntingtin protein accelerates this aggregation, and while there have been several mechanisms proposed, its exact role in this process remains largely unknown.<ref name="10.1038/nchembio.279"/> Folding@home has simulated this and other fragments to clarify their roles in the disease.<ref name="forum: 8021 in beta"/> Since 2008, its drug design methods for Alzheimer's disease have been applied to Huntington's.<ref name="diseases FAQ"/>

=== Cancer ===
More than half of all known cancers involve [[mutations]] of [[p53]], a [[tumor suppressor]] protein present in every cell which regulates the [[cell cycle]] and signals for [[cell death]] in the event of damage to [[DNA]]. Specific mutations in p53 can disrupt these functions, allowing an abnormal cell to continue growing unchecked, resulting in the development of [[tumors]]. Analysis of these mutations helps explain the root causes of p53-related cancers.<ref name="10.1126/science.1905840"/> In 2004, Folding@home was used to perform the first molecular dynamics study of the refolding of p53's [[protein dimer]] in an [[water model|all-atom simulation of water]]. The simulation's results agreed with experimental observations and gave insights into the refolding of the dimer that were formerly unobtainable.<ref name="10.1016/j.jmb.2004.10.083"/> This was the first [[peer review]]ed publication on cancer from a distributed computing project.<ref name="FAH publishes cancer results"/> The following year, Folding@home powered a new method to identify the amino acids crucial for the stability of a given protein, which was then used to study mutations of p53. The method was reasonably successful in identifying cancer-promoting mutations and determined the effects of specific mutations which could not otherwise be measured experimentally.<ref name="10.1016/j.jmb.2005.12.083"/>

Folding@home is also used to study [[chaperone (protein)|protein chaperones]],<ref name="diseases FAQ"/> [[heat shock protein]]s which play essential roles in cell survival by assisting with the folding of other proteins in the [[Macromolecular crowding|crowded]] and chemically stressful environment within a cell. Rapidly growing cancer cells rely on specific chaperones, and some chaperones play key roles in [[chemotherapy]] resistance. Inhibitions to these specific chaperones are seen as potential modes of action for efficient chemotherapy drugs or for reducing the spread of cancer.<ref name="10.1016/j.biopha.2011.04.025"/> Using Folding@home and working closely with the Center for Protein Folding Machinery, the Pande lab hopes to find a drug which inhibits those chaperones involved in cancerous cells.<ref name="typepad: nanomedicine ce"/> Researchers are also using Folding@home to study other molecules related to cancer, such as the enzyme [[Src kinase]], and some forms of the [[Engrailed (gene)|engrailed]] [[homeodomain]]: a large protein which may be involved in many diseases, including cancer.<ref name="typepad: protomol b4"/><ref name="description: 180"/> In 2011, Folding@home began simulations of the dynamics of the small [[Trefoil knot fold|knottin]] protein EETI, which can identify [[carcinoma]]s in [[medical imaging|imaging scan]]s by binding to [[cell surface receptor|surface receptor]]s of cancer cells.<ref name="forum: 7600 in beta"/><ref name="description: 7600"/>

[[Interleukin 2]] (IL-2) is a protein that helps [[T cell]]s of the [[immune system]] attack pathogens and tumors. However, its use as a cancer treatment is restricted due to serious side effects such as [[pulmonary edema]]. IL-2 binds to these pulmonary cells differently than it does to T cells, so IL-2 research involves understanding the differences between these binding mechanisms. In 2012, Folding@home assisted with the discovery of a mutant form of IL-2 which is three hundred times more effective in its immune system role but carries fewer side effects. In experiments, this altered form significantly outperformed natural IL-2 in impeding tumor growth. [[Pharmaceutical companies]] have expressed interest in the mutant molecule, and the [[National Institutes of Health]] are testing it against a large variety of tumor models to try to accelerate its development as a therapeutic.<ref name="scientists boost IL-2 potency"/><ref name="10.1038/nature10975"/>

=== Osteogenesis imperfecta ===
[[Osteogenesis imperfecta]], known as brittle bone disease, is an incurable genetic bone disorder which can be lethal. Those with the disease are unable to make functional connective bone tissue. This is most commonly due to a mutation in [[Type-I collagen]],<ref name="10.1016/S0140-6736(04)16051-0"/> which fulfills a variety of structural roles and is the most abundant protein in [[mammal]]s.<ref name="978-0-387-73905-2"/> The mutation causes a deformation in [[Collagen helix|collagen's triple helix structure]], which if not naturally destroyed, leads to abnormal and weakened bone tissue.<ref name="10.1016/j.bpj.2009.04.059"/> In 2005, Folding@home tested a new [[quantum mechanical]] method that improved upon prior simulation methods, and which may be useful for future computing studies of collagen.<ref name="10.1002/jcc.20301"/> Although researchers have used Folding@home to study collagen folding and misfolding, the interest stands as a pilot project compared to [[Alzheimer]]'s and Huntington's research.<ref name="diseases FAQ"/>

=== Viruses ===
Folding@home is assisting in research towards preventing some [[virus]]es, such as [[influenza]] and [[HIV]], from recognizing and entering [[Cell (biology)|biological cells]].<ref name="diseases FAQ"/> In 2011, Folding@home began simulations of the dynamics of the enzyme [[RNase H]], a key component of HIV, to try to design drugs to deactivate it.<ref name="forum: 10125"/> Folding@home has also been used to study [[membrane fusion]], an essential event for [[viral entry|viral infection]] and a wide range of biological functions. This fusion involves [[conformational change]]s of viral fusion proteins and [[protein docking]],<ref name="978-0-340-66316-5"/> but the exact molecular mechanisms behind fusion remain largely unknown.<ref name="10.1039/c0cs00115e"/> Fusion events may consist of over a half million atoms interacting for hundreds of microseconds. This complexity limits typical computer simulations to about ten thousand atoms over tens of nanoseconds: a difference of several orders of magnitude.<ref name="10.1038/cr.2010.57"/> The development of models to predict the mechanisms of membrane fusion will assist in the scientific understanding of how to target the process with antiviral drugs.<ref name="Peter Kasson"/> In 2006, scientists applied Markov state models and the Folding@home network to discover two pathways for fusion and gain other mechanistic insights.<ref name="10.1038/cr.2010.57"/>

Following detailed simulations from Folding@home of small cells known as [[vesicle (biology)|vesicles]], in 2007, the Pande lab introduced a new computing method to measure the [[topology]] of its structural changes during fusion.<ref name="10.1093/bioinformatics/btm250"/> In 2009, researchers used Folding@home to study mutations of [[Hemagglutinin (influenza)|influenza hemagglutinin]], a protein that attaches a virus to its [[Host (biology)|host]] cell and assists with viral entry. Mutations to hemagglutinin affect [[binding affinity|how well the protein binds]] to a host's [[cell surface receptor]] molecules, which determines how [[infectivity|infective]] the virus strain is to the host organism. Knowledge of the effects of hemagglutinin mutations assists in the development of [[antiviral drug]]s.<ref name="10.1021/ja904557w"/><ref name="19209725, 2811693"/> As of 2012, Folding@home continues to simulate the folding and interactions of hemagglutinin, complementing experimental studies at the [[University of Virginia]].<ref name="diseases FAQ"/><ref name="typepad: kasson update"/>

In March 2020, Folding@home launched a program to assist researchers around the world who are working on finding a cure and learning more about the [[COVID-19 pandemic|coronavirus pandemic]]. The initial wave of projects simulate potentially druggable protein targets from SARS-CoV-2 virus, and the related SARS-CoV virus, about which there is significantly more data available.<ref name="tomshw-fah">{{cite web |last1=Broekhuijsen |first1=Niels |title=Help Cure Coronavirus with Your PC's Leftover Processing Power |url=https://www.tomshardware.com/news/folding-fight-coronavirus |website=Tom's Hardware |access-date=March 12, 2020 |date=March 3, 2020}}</ref><ref name="fah-newspost">{{cite web |last1=Bowman |first1=Greg |title=Folding@home takes up the fight against COVID-19 / 2019-nCoV |url=https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/ |website=Folding@home |access-date=March 12, 2020 |date=February 27, 2020}}</ref><ref>{{Cite web | url=https://www.hpcwire.com/2020/03/16/foldinghome-turns-its-massive-crowdsourced-computer-network-against-covid-19/ |title = Folding@home Turns Its Massive Crowdsourced Computer Network Against COVID-19|date = March 16, 2020}}</ref>

=== Drug design ===
[[Drug]]s function by [[ligand binding|binding]] to [[binding site|specific locations]] on target molecules and causing some desired change, such as disabling a target or causing a [[conformational change]]. Ideally, a drug should act very specifically, and bind only to its target without interfering with other biological functions. However, it is difficult to precisely determine where and [[binding affinity|how tightly]] two molecules will bind. Due to limits in computing power, current ''[[in silico]]'' methods usually must trade speed for [[accuracy]]; e.g., use rapid [[protein docking]] methods instead of computationally costly [[free energy calculation]]s. Folding@home's computing performance allows researchers to use both methods, and evaluate their efficiency and reliability.<ref name="Press FAQ"/><ref name="typepad: drug design methods"/><ref name="10.1063/1.2221680"/> Computer-assisted drug design has the potential to expedite and lower the costs of drug discovery.<ref name="10.1093/bib/bbp023"/> In 2010, Folding@home used MSMs and free energy calculations to predict the native state of the [[villin]] protein to within 1.8 [[angstrom]] (Å) [[root mean square deviation]] (RMSD) from the [[crystalline structure]] experimentally determined through [[X-ray crystallography]]. This accuracy has implications to future [[protein structure prediction]] methods, including for [[intrinsically unstructured proteins]].<ref name="10.1038/cr.2010.57"/> Scientists have used Folding@home to research [[drug resistance]] by studying [[vancomycin]], an antibiotic [[drug of last resort]], and [[beta-lactamase]], a protein that can break down antibiotics like [[penicillin]].<ref name="description: 10721"/><ref name="typepad: drug targets"/>

Chemical activity occurs along a protein's [[active site]]. Traditional drug design methods involve tightly binding to this site and blocking its activity, under the assumption that the target protein exists in one rigid structure. However, this approach works for approximately only 15% of all proteins. Proteins contain [[allosteric site]]s which, when bound to by small molecules, can alter a protein's conformation and ultimately affect the protein's activity. These sites are attractive drug targets, but locating them is very [[Analysis of algorithms|computationally costly]]. In 2012, Folding@home and MSMs were used to identify allosteric sites in three medically relevant proteins: beta-lactamase, [[interleukin-2]], and [[RNase H]].<ref name="typepad: drug targets"/><ref name="10.1073/pnas.1209309109"/>

Approximately half of all known [[antibiotic]]s interfere with the workings of a bacteria's [[ribosome]], a large and complex biochemical machine that performs [[protein biosynthesis]] by [[translation (biology)|translating]] [[messenger RNA]] into proteins. [[Macrolide antibiotics]] clog the ribosome's exit tunnel, preventing synthesis of essential bacterial proteins. In 2007, the Pande lab received a [[grant (money)|grant]] to study and design new antibiotics.<ref name="diseases FAQ"/> In 2008, they used Folding@home to study the interior of this tunnel and how specific molecules may affect it.<ref name="10.1073/pnas.0801795105"/> The full structure of the ribosome was determined only as of 2011, and Folding@home has also simulated [[ribosomal protein]]s, as many of their functions remain largely unknown.<ref name="description: 5765"/>

== Patterns of participation ==
Like other [[distributed computing]] projects, Folding@home is an online [[citizen science]] project. In these projects non-specialists contribute computer processing power or help to analyze data produced by professional scientists. Participants receive little or no obvious reward.

Research has been carried out into the motivations of citizen scientists and most of these studies have found that participants are motivated to take part because of altruistic reasons; that is, they want to help scientists and make a contribution to the advancement of their research.<ref>{{Cite journal|last1=Raddick|first1=M. Jordan|last2=Bracey|first2=Georgia|last3=Gay|first3=Pamela L.|last4=Lintott|first4=Chris J.|last5=Murray|first5=Phil|last6=Schawinski|first6=Kevin|last7=Szalay|first7=Alexander S.|last8=Vandenberg|first8=Jan|date=December 2010|title=Galaxy Zoo: Exploring the Motivations of Citizen Science Volunteers|journal=Astronomy Education Review|volume=9|issue=1|pages=010103|doi=10.3847/AER2009036|arxiv=0909.2925|bibcode=2010AEdRv...9a0103R|s2cid=118372704 |doi-access=free }}</ref><ref>{{Cite book|title=Online citizen science and the widening of academia : distributed engagement with research and knowledge production|last=Vickie|first=Curtis|isbn=9783319776644|publisher=Springer International Publishing|location=Cham, Switzerland|oclc=1034547418|date = April 20, 2018}}</ref><ref>{{Cite book|last1=Nov|first1=Oded|last2=Arazy|first2=Ofer|last3=Anderson|first3=David|title=Proceedings of the 2011 iConference |chapter=Dusting for science |date=2011|chapter-url=http://portal.acm.org/citation.cfm?doid=1940761.1940771|location=Seattle, Washington|publisher=ACM Press|pages=68–74|doi=10.1145/1940761.1940771|isbn=9781450301213|series=IConference '11|s2cid=12219985}}</ref><ref>{{Cite journal|last=Curtis|first=Vickie|date=December 2015|title=Motivation to Participate in an Online Citizen Science Game: A Study of Foldit|journal=Science Communication|volume=37|issue=6|pages=723–746|doi=10.1177/1075547015609322|s2cid=1345402|issn=1075-5470|url=http://oro.open.ac.uk/44708/1/V%20Curtis%20Foldit%20Manuscript%20Oct%202015.pdf}}</ref> Many participants in citizen science have an underlying interest in the topic of the research and gravitate towards projects that are in disciplines of interest to them. Folding@home is no different in that respect.<ref name=":0">{{Cite journal|last=Curtis|first=Vickie|date=April 27, 2018|title=Patterns of Participation and Motivation in Folding@home: The Contribution of Hardware Enthusiasts and Overclockers|journal=Citizen Science: Theory and Practice|volume=3|issue=1|pages=5|doi=10.5334/cstp.109|issn=2057-4991|doi-access=free}}</ref> Research carried out recently on over 400 active participants revealed that they wanted to help make a contribution to research and that many had friends or relatives affected by the diseases that the Folding@home scientists investigate.

Folding@home attracts participants who are computer hardware enthusiasts. These groups bring considerable expertise to the project and are able to build computers with advanced processing power.<ref>{{Cite journal|last=Colwell|first=B.|date=March 2004|title=The Zen of overclocking|journal=Computer|volume=37|issue=3|pages=9–12|doi=10.1109/MC.2004.1273994|s2cid=21582410|issn=0018-9162}}</ref>{{Request quotation|date=July 2022}} Other distributed computing projects attract these types of participants and projects are often used to benchmark the performance of modified computers, and this aspect of the hobby is accommodated through the competitive nature of the project. Individuals and teams can compete to see who can process the most computer processing units (CPUs).

This latest research on Folding@home involving interview and ethnographic observation of online groups showed that teams of hardware enthusiasts can sometimes work together, sharing best practice with regard to maximizing processing output. Such teams can become [[Communities of Practice|communities of practice]], with a shared language and online culture. This pattern of participation has been observed in other distributed computing projects.<ref>{{Cite journal|last1=Kloetzer|first1=Laure|last2=Da Costa|first2=Julien|last3=Schneider|first3=Daniel K.|date=December 31, 2016|title=Not so passive: engagement and learning in Volunteer Computing projects|journal=Human Computation|volume=3|issue=1|pages=25–68|doi=10.15346/hc.v3i1.4|issn=2330-8001|doi-access=free}}</ref><ref>{{Cite journal|last1=Darch Peter|last2=Carusi Annamaria|date=September 13, 2010|title=Retaining volunteers in volunteer computing projects|journal=Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences|volume=368|issue=1926|pages=4177–4192|doi=10.1098/rsta.2010.0163|pmid=20679130|bibcode=2010RSPTA.368.4177D|s2cid=1675353 |doi-access=}}</ref>

Another key observation of Folding@home participants is that many are male.<ref name=":0" /> This has also been observed in other distributed projects. Furthermore, many participants work in computer and technology-based jobs and careers.<ref name=":0" /><ref>{{Cite web|url=https://www.worldcommunitygrid.org/about_us/viewNewsArticle.do?articleId=323|title=2013 Member Study: Findings and Next Steps|publisher=World Community Grid}}</ref><ref>{{Cite journal|last=Krebs|first=Viola|date=January 31, 2010|title=Motivations of cybervolunteers in an applied distributed computing environment: MalariaControl.net as an example|journal=First Monday|volume=15|issue=2|doi=10.5210/fm.v15i2.2783 |doi-access= free}}</ref>

Not all Folding@home participants are hardware enthusiasts. Many participants run the project software on unmodified machines and do take part competitively. By January 2020, the number of users was down to 30,000.<ref>{{cite web | url=https://arstechnica.com/science/2020/04/how-the-pandemic-revived-a-distributed-computing-project-and-made-history/ | title=The coronavirus pandemic turned Folding@Home into an exaFLOP supercomputer | date=April 14, 2020 }}</ref> However, it is difficult to ascertain what proportion of participants are hardware enthusiasts. Although, according to the project managers, the contribution of the enthusiast community is substantially larger in terms of processing power.<ref>{{Cite book|url=http://oro.open.ac.uk/42239/1/Vickie%20Curtis%20PhD%20Thesis%20Oct%202014.pdf|title=Online citizen science projects: an exploration of motivation, contribution and participation, PhD Thesis|last=Curtis|first=Vickie|publisher=The Open University|year=2015|location=United Kingdom}}</ref>

=== Performance ===
[[File:Folding@home and Supercomputer Computational Powers.png|thumb|Computing power of Folding@home and the fastest supercomputer from April 2004 to October 2012. Between June 2007 and June 2011, Folding@home (red) exceeded the performance of [[Top500]]'s fastest supercomputer (black). However it was eclipsed by [[K computer]] in November 2011 and [[Blue Gene/Q]] in June 2012.]]

Supercomputer FLOPS performance is assessed by running the legacy [[LINPACK]] benchmark. This short-term testing has difficulty in accurately reflecting sustained performance on real-world tasks because LINPACK more efficiently maps to supercomputer hardware. Computing systems vary in architecture and design, so direct comparison is difficult. Despite this, FLOPS remain the primary speed metric used in supercomputing.<ref>{{harvnb|Mims|2010}}</ref>{{Request quotation|date=April 2020}} In contrast, Folding@home determines its FLOPS using [[wall-clock time]] by measuring how much time its work units take to complete.<ref>{{harvnb|Pande|2008}}: "Wall clock time is in the end the only thing that matters and that's why we benchmark on wall clock (and why in our papers, we emphasize wall clock)."</ref>

On September 16, 2007, due in large part to the participation of PlayStation 3 consoles, the Folding@home project officially attained a sustained performance level higher than one native [[Petascale computing|petaFLOPS]], becoming the first computing system of any kind to do so.<ref name="typepad: crossing 1 PF"/><ref name="10.1016/j.cub.2012.01.008"/> [[Top500]]'s fastest supercomputer at the time was [[BlueGene/L]], at 0.280 petaFLOPS.<ref name="Top500 June 2007"/> The following year, on May 7, 2008, the project attained a sustained performance level higher than two native petaFLOPS,<ref name="FAH reaches 2 PF"/> followed by the three and four native petaFLOPS milestones in August 2008<ref name="Nvidia-FAH milestone"/><ref name="3 PF barrier"/> and September 28, 2008 respectively.<ref name="past 4 petaFLOPS"/> On February 18, 2009, Folding@home achieved five native petaFLOPS,<ref name="typepad: FAH passes 5 PF"/><ref name="crossing 5 PF barrier"/> and was the first computing project to meet these five levels.<ref name="Community Grid Computing"/><ref name="review of FAH"/> In comparison, November 2008's fastest supercomputer was [[IBM]]'s [[IBM Roadrunner|Roadrunner]] at 1.105 petaFLOPS.<ref name="Top500 November 2008"/> On November 10, 2011, Folding@home's performance exceeded six native petaFLOPS with the equivalent of nearly eight x86 petaFLOPS.<ref name="10.1016/j.cub.2012.01.008"/><ref name="6 petaFLOPS"/> In mid-May 2013, Folding@home attained over seven native petaFLOPS, with the equivalent of 14.87 x86 petaFLOPS. It then reached eight native petaFLOPS on June 21, followed by nine on September 9 of that year, with 17.9 x86 petaFLOPS.<ref name="FAH stats doc"/> On May 11, 2016 Folding@home announced that it was moving towards reaching the 100 x86 petaFLOPS mark.<ref>{{cite web|title=100 Petaflops nearly reached|url=https://foldingathome.org/home/closing-in-on-100-petaflops|publisher=foldingathome.org|access-date=August 9, 2016|date=May 11, 2016}}</ref>

Further use grew from increased awareness and participation in the project from the coronavirus pandemic in 2020. On March 20, 2020 Folding@home announced via Twitter that it was running with over 470 native petaFLOPS,<ref>{{Cite web|url=https://twitter.com/drGregBowman/status/1241037866215657472|title=Amazing! @foldingathome now has over 470 petaFLOPS of compute power. To put that in perspective, that's more than 2x the peak performance of the Summit super computer!|last=Bowman|first=Greg|date=March 20, 2020|website=@drGregBowman|language=en|access-date=March 20, 2020}}</ref> the equivalent of 958 x86 petaFLOPS.<ref>{{Cite web|url=https://stats.foldingathome.org/os|title=Folding@home stats report|date=March 20, 2020|archive-url=https://web.archive.org/web/20200320191855/https://stats.foldingathome.org/os|access-date=March 20, 2020|archive-date=March 20, 2020}}</ref> By March 25 it reached 768 petaFLOPS, or 1.5 x86 exaFLOPS, making it the first [[Exascale computing|exaFLOP computing system]].<ref>{{cite web | url = https://www.anandtech.com/show/15661/folding-at-home-reaches-exascale-1000000000000000000-operations-per-second-for-covid-19 | title = Folding@Home Reaches Exascale: 1,500,000,000,000,000,000 Operations Per Second for COVID-19 | first = Anton | last= Shilov | date =March 25, 2020 | access-date = March 26, 2020 | work = [[Anandtech]] }}</ref>

{{as of|2024|12|23}}, the computing power of Folding@home stands at 14.3 petaFLOPS, or 27.5 x86 petaFLOPS.<ref>{{Cite web |url=https://stats.foldingathome.org/os |title=Folding@home stats report |access-date=December 23, 2024}}</ref>

=== Points ===
Similarly to other distributed computing projects, Folding@home quantitatively assesses user computing contributions to the project through a credit system.<ref name="Points FAQ"/> All units from a given protein project have uniform base credit, which is determined by benchmarking one or more work units from that project on an official reference machine before the project is released.<ref name="Points FAQ"/> Each user receives these base points for completing every work unit, though through the use of a passkey they can receive added bonus points for reliably and rapidly completing units which are more demanding computationally or have a greater scientific priority.<ref name="Passkey FAQ"/><ref name="SMP2 release"/> Users may also receive credit for their work by clients on multiple machines.<ref name="Main FAQ"/> This point system attempts to align awarded credit with the value of the scientific results.<ref name="Points FAQ"/>

Users can register their contributions under a team, which combine the points of all their members. A user can start their own team, or they can join an existing team. In some cases, a team may have their own community-driven sources of help or recruitment such as an [[Internet forum]].<ref name="Extreme overclocking forum"/> The points can foster friendly competition between individuals and teams to compute the most for the project, which can benefit the folding community and accelerate scientific research.<ref name="Points FAQ"/><ref name="10.1109/IPDPS.2009.5160922"/><ref name="MaximumPC Chimp Challenge"/> Individual and team statistics are posted on the Folding@home website.<ref name="Points FAQ"/>

If a user does not form a new team, or does not join an existing team, that user automatically becomes part of a "Default" team. This "Default" team has a team number of "0". Statistics are accumulated for this "Default" team as well as for specially named teams.

== Software ==
Folding@home software at the user's end involves three primary components: work units, cores, and a client.

=== Work units ===
A work unit is the protein data that the client is asked to process. Work units are a fraction of the simulation between the states in a [[Markov model]]. After the work unit has been downloaded and completely processed by a volunteer's computer, it is returned to Folding@home servers, which then award the volunteer the credit points. This cycle repeats automatically.<ref name="10.1109/IPDPS.2009.5160922"/> All work units have associated deadlines, and if this deadline is exceeded, the user may not get credit and the unit will be automatically reissued to another participant. As protein folding occurs serially, and many work units are generated from their predecessors, this allows the overall simulation process to proceed normally if a work unit is not returned after a reasonable period of time. Due to these deadlines, the minimum system requirement for Folding@home is a Pentium&nbsp;3 450&nbsp;MHz CPU with [[Streaming SIMD Extensions]] (SSE).<ref name="Main FAQ"/> However, work units for high-performance clients have a much shorter deadline than those for the uniprocessor client, as a major part of the scientific benefit is dependent on rapidly completing simulations.<ref name="SMP FAQ"/>

Before public release, work units go through several [[quality assurance]] steps to keep problematic ones from becoming fully available. These testing stages include internal, beta, and advanced, before a final full release across Folding@home.<ref name="typepad: more transparency"/> Folding@home's work units are normally processed only once, except in the rare event that errors occur during processing. If this occurs for three different users, the unit is automatically pulled from distribution.<ref name="forum: Gromacs cannot continue"/><ref name="forum: 6803(4,66,255)"/> The Folding@home support forum can be used to differentiate between issues arising from problematic hardware and bad work units.<ref name="forum: troubleshooting bad WUs"/>

=== Cores ===
{{main|List of Folding@home cores}}
Specialized molecular dynamics programs, referred to as "FahCores" and often abbreviated "cores", perform the calculations on the work unit as a [[background process]]. A large majority of Folding@home's cores are based on [[GROMACS]],<ref name="10.1109/IPDPS.2009.5160922"/> one of the fastest and most popular molecular dynamics software packages, which largely consists of manually optimized [[assembly language]] code and hardware optimizations.<ref name="10.1002/jcc.20703"/><ref name="10.1021/ct700301q"/> Although GROMACS is [[open-source software]] and there is a cooperative effort between the Pande lab and GROMACS developers, Folding@home uses a [[closed-source]] license to help ensure data validity.<ref name="Gromacs FAQ"/> Less active cores include ProtoMol and SHARPEN. Folding@home has used [[AMBER]], [[CPMD]], [[Desmond (software)|Desmond]], and [[TINKER]], but these have since been retired and are no longer in active service.<ref name="Open Source FAQ"/><ref name="FAQ index"/><ref name="typepad: update on new FahCores"/> Some of these cores perform [[explicit water model|explicit solvation]] calculations in which the surrounding [[solvent]] (usually water) is modeled atom-by-atom; while others perform [[implicit solvation]] methods, where the solvent is treated as a mathematical continuum.<ref name="10.1002/jcc.21209"/><ref name="Petaflop FAQ"/> The core is separate from the client to enable the scientific methods to be updated automatically without requiring a client update. The cores periodically create calculation [[application checkpointing|checkpoints]] so that if they are interrupted they can resume work from that point upon startup.<ref name="10.1109/IPDPS.2009.5160922"/>

=== Client ===

[[File:Folding@home Fedora25.png|thumb|Folding@home running on Fedora 25]]

A Folding@home participant installs a [[client (computing)|client]] [[computer program|program]] on their [[personal computer]]. The user interacts with the client, which manages the other software components in the background. Through the client, the user may pause the folding process, open an event log, check the work progress, or view personal statistics.<ref name="Uni Guide"/> The computer clients run continuously in the [[background (computer software)|background]] at a very low priority, using idle processing power so that normal computer use is unaffected.<ref name="Main FAQ"/> The maximum CPU use can be adjusted via client settings.<ref name="Uni Guide"/><ref name="forum: can FAH damage PC?"/> The client connects to a Folding@home [[server (computing)|server]] and retrieves a work unit and may also download the appropriate core for the client's settings, operating system, and the underlying hardware architecture. After processing, the work unit is returned to the Folding@home servers. Computer clients are tailored to [[uniprocessor]] and [[multi-core processor]] systems, and [[graphics processing unit]]s. The diversity and power of each [[hardware architecture]] provides Folding@home with the ability to efficiently complete many types of simulations in a timely manner (in a few weeks or months rather than years), which is of significant scientific value. Together, these clients allow researchers to study biomedical questions formerly considered impractical to tackle computationally.<ref name="Press FAQ"/><ref name="10.1109/IPDPS.2009.5160922"/><ref name="SMP FAQ"/>

Professional software developers are responsible for most of Folding@home's code, both for the client and server-side. The development team includes programmers from [[Nvidia]], [[ATI Technologies|ATI]], [[Sony]], and Cauldron Development.<ref name="typepad: how does dev get done"/> Clients can be downloaded only from the official Folding@home website or its commercial partners, and will only interact with Folding@home computer files. They will upload and download data with Folding@home's data servers (over [[Computer port (software)|port]]&nbsp;8080, with 80 as an alternate), and the communication is verified using 2048-bit [[digital signature]]s.<ref name="Main FAQ"/><ref name="Uninstall"/> While the client's [[graphical user interface]] (GUI) is open-source,<ref name="FAHControl source code"/> the client is [[proprietary software]] citing security and scientific integrity as the reasons.<ref name="FAH license"/><ref name="forum: FAH EULA"/><ref name="help ubuntu"/>

However, this rationale of using proprietary software is disputed since while the license could be enforceable in the legal domain retrospectively, it does not practically prevent the modification (also known as [[Patch (computing)|patching]]) of the executable [[binary file]]s. Likewise, [[binary-only software|binary-only]] distribution does not prevent the malicious modification of executable binary-code, either through a [[man-in-the-middle attack]] while being downloaded via the internet,<ref>{{Cite web|url=https://www.leviathansecurity.com/blog/the-case-of-the-modified-binaries|title=The Case of the Modified Binaries|website=Leviathan Security}}</ref> or by the redistribution of binaries by a third-party that have been previously modified either in their binary state (i.e. [[Patch (computing)|patched]]),<ref>{{Cite web|url=http://www.blackhat.com/presentations/bh-usa-02/clowes/bh-us-02-clowes-binaries.ppt|title=Fixing/Making Holes in ELF Binaries/Programs - Black Hat}}</ref> or by decompiling<ref>probably using tools such as [https://github.com/thorkill/eresi ERESI] {{Webarchive|url=https://web.archive.org/web/20180707212104/https://github.com/thorkill/eresi |date=July 7, 2018 }}</ref> and recompiling them after modification.<ref>{{Cite web|url=https://stackoverflow.com/questions/4309771/how-to-disassemble-modify-and-then-reassemble-a-linux-executable|title=x86 - How to disassemble, modify and then reassemble a Linux executable?|website=Stack Overflow}}</ref><ref>{{Cite web|url=https://reverseengineering.stackexchange.com/questions/185/how-do-i-add-functionality-to-an-existing-binary-executable|title=linux - How do I add functionality to an existing binary executable?|website=Reverse Engineering Stack Exchange}}</ref> These modifications are possible unless the binary files&nbsp;– and the transport channel&nbsp;– are [[digital signature|signed]] and the recipient person/system is able to verify the digital signature, in which case unwarranted modifications should be detectable, but not always.<ref>{{cite web |url=https://www.blackhat.com/docs/us-16/materials/us-16-Nipravsky-Certificate-Bypass-Hiding-And-Executing-Malware-From-A-Digitally-Signed-Executable-wp.pdf |title=Certificate Bypass: Hiding and Executing Malware from a Digitally Signed Executable |publisher=[[Deep Instinct]] |website=BlackHat.com |date=August 2016}}</ref> Either way, since in the case of Folding@home the input data and output result processed by the client-software are both digitally signed,<ref name="Main FAQ"/><ref name="Uninstall"/> the integrity of work can be verified independently from the integrity of the client software itself.

Folding@home uses the [[Cosm (software)|Cosm]] software libraries for networking.<ref name="10.1109/IPDPS.2009.5160922"/><ref name="typepad: how does dev get done"/> Folding@home was launched on October&nbsp;1, 2000, and was the first [[distributed computing]] project aimed at bio-molecular systems.<ref name="10.1039/C1CP22100K"/> Its first client was a [[screensaver]], which would run while the computer was not otherwise in use.<ref name="10.1126/science.290.5498.1903"/><ref name="Executive summary"/> In 2004, the Pande lab collaborated with [[David P. Anderson]] to test a supplemental client on the open-source [[Berkeley Open Infrastructure for Network Computing|BOINC]] framework. This client was released to closed beta in April 2005;<ref name="FAH for BOINC soon"/> however, the method became unworkable and was shelved in June 2006.<ref name="High-Per FAQ"/>

==== Graphics processing units ====
The specialized hardware of [[graphics processing unit]]s (GPU) is designed to accelerate rendering of 3-D&nbsp;graphics applications such as video games and can significantly outperform CPUs for some types of calculations. GPUs are one of the most powerful and rapidly growing computing platforms, and many scientists and researchers are pursuing [[general-purpose computing on graphics processing units]] (GPGPU). However, GPU hardware is difficult to use for non-graphics tasks and usually requires significant algorithm restructuring and an advanced understanding of the underlying architecture.<ref name="10.1111/j.1467-8659.2007.01012.x"/> Such customization is challenging, more so to researchers with limited software development resources. Folding@home uses the [[open-source software|open-source]] [[OpenMM]] [[library (computing)|library]], which uses a [[bridge pattern|bridge design pattern]] with two [[application programming interface]] (API) levels to interface molecular simulation software to an underlying hardware architecture. With the addition of hardware optimizations, OpenMM-based GPU simulations need no significant modification but achieve performance nearly equal to hand-tuned GPU code, and greatly outperform CPU implementations.<ref name="10.1002/jcc.21209"/><ref name="10.1109/MCSE.2010.27"/>

Before 2010, the computing reliability of GPGPU consumer-grade hardware was largely unknown, and circumstantial evidence related to the lack of built-in [[error detection and correction]] in GPU memory raised reliability concerns. In the first large-scale test of GPU scientific accuracy, a 2010 study of over 20,000 hosts on the Folding@home network detected [[soft error]]s in the memory subsystems of two-thirds of the tested GPUs. These errors strongly correlated to board architecture, though the study concluded that reliable GPU computing was very feasible as long as attention is paid to the hardware traits, such as software-side error detection.<ref name="10.1109/CCGRID.2010.84"/>

The first generation of Folding@home's GPU client (GPU1) was released to the public on October&nbsp;2, 2006,<ref name="High-Per FAQ"/> delivering a 20–30 times speedup for some calculations over its CPU-based [[GROMACS]] counterparts.<ref name="ATI FAQ"/> It was the first time GPUs had been used for either distributed computing or major molecular dynamics calculations.<ref name="typepad: GPU news"/><ref name="978-3-642-14389-2"/> GPU1 gave researchers significant knowledge and experience with the development of [[General-purpose computing on graphics processing units|GPGPU]] software, but in response to scientific inaccuracies with [[DirectX]], on April&nbsp;10, 2008, it was succeeded by GPU2, the second generation of the client.<ref name="ATI FAQ"/><ref name="typepad: GPU2 open beta"/> Following the introduction of GPU2, GPU1 was officially retired on June&nbsp;6.<ref name="ATI FAQ"/> Compared to GPU1, GPU2 was more scientifically reliable and productive, ran on [[ATI (brand)|ATI]] and [[CUDA]]-enabled [[Nvidia]] GPUs, and supported more advanced algorithms, larger proteins, and real-time visualization of the protein simulation.<ref name="typepad: GPU2 goes live"/><ref name="typepad: GPU2 going well"/> Following this, the third generation of Folding@home's GPU client (GPU3) was released on May&nbsp;25, 2010. While [[Backward compatibility|backward compatible]] with GPU2, GPU3 was more stable, efficient, and flexibile in its scientific abilities,<ref name="typepad: GPU3 prep"/> and used OpenMM on top of an [[OpenCL]] framework.<ref name="typepad: GPU3 prep"/><ref name="typepad: GPU3 open beta"/> Although these GPU3 clients did not natively support the operating systems [[Linux]] and [[macOS]], Linux users with Nvidia graphics cards were able to run them through the [[Wine (software)|Wine]] software application.<ref name="forum: 7.1.38 released"/><ref name="forum: GPU3 headless guide"/> GPUs remain Folding@home's most powerful platform in [[FLOPS]]. As of November 2012, GPU clients account for 87% of the entire project's x86 FLOPS throughput.<ref name="FAH osstats2"/>

Native support for Nvidia and AMD graphics cards under Linux was introduced with FahCore&nbsp;17, which uses OpenCL rather than CUDA.<ref name="forum: core17 Linux"/>

==== PlayStation 3 ====
{{further|Life with PlayStation}}
[[File:LifeWithPlayStation Folding.jpg|thumb|The PlayStation 3's ''Life With PlayStation'' client displayed a 3-D animation of the protein being folded.]]

From March 2007 until November 2012, Folding@home took advantage of the computing power of [[PlayStation 3]]s. At the time of its inception, its main [[stream processing|streaming]] [[Cell (microprocessor)|Cell processor]] delivered a 20 times speed increase over PCs for some calculations, processing power which could not be found on other systems such as the [[Xbox 360]].<ref name="Press FAQ"/><ref name="Biotech 27"/> The PS3's high speed and efficiency introduced other opportunities for worthwhile optimizations according to [[Amdahl's law]], and significantly changed the tradeoff between computing efficiency and overall accuracy, allowing the use of more complex molecular models at little added computing cost.<ref name="10.1002/jcc.21054"/> This allowed Folding@home to run biomedical calculations that would have been otherwise infeasible computationally.<ref name="cnn ps3"/>

The PS3 client was developed in a collaborative effort between [[Sony]] and the Pande lab and was first released as a standalone client on March&nbsp;23, 2007.<ref name="Press FAQ"/><ref name="PS3 to study cancer"/> Its release made Folding@home the first distributed computing project to use PS3s.<ref name="PS3 research project"/> On September&nbsp;18 of the following year, the PS3 client became a channel of [[Life with PlayStation]] on its launch.<ref name="Life With PS3 live"/><ref name="typepad: life with PS"/> In the types of calculations it can perform, at the time of its introduction, the client fit in between a CPU's flexibility and a GPU's speed.<ref name="10.1109/IPDPS.2009.5160922"/> However, unlike clients running on [[personal computer]]s, users were unable to perform other activities on their PS3 while running Folding@home.<ref name="cnn ps3"/> The PS3's uniform console environment made [[technical support]] easier and made Folding@home more [[user friendly]].<ref name="Press FAQ"/> The PS3 also had the ability to stream data quickly to its GPU, which was used for real-time atomic-level visualizing of the current protein dynamics.<ref name="10.1002/jcc.21054"/>

On November 6, 2012, Sony ended support for the Folding@home PS3 client and other services available under Life with PlayStation. Over its lifetime of five years and seven months, more than 15&nbsp;million users contributed over 100&nbsp;million hours of computing to Folding@home, greatly assisting the project with disease research. Following discussions with the Pande lab, Sony decided to terminate the application. Pande considered the PlayStation 3 client a "game changer" for the project.<ref name="PS3 FAQ"/><ref name="PS3 4.30 update, drop F@h"/><ref name="LWP termination"/>

==== Multi-core processing client ====
Folding@home can use the [[parallel computing]] abilities of modern multi-core processors. The ability to use several CPU cores simultaneously allows completing the full simulation far faster. Working together, these CPU cores complete single work units proportionately faster than the standard uniprocessor client. This method is scientifically valuable because it enables much longer simulation trajectories to be performed in the same amount of time, and reduces the traditional difficulties of scaling a large simulation to many separate processors.<ref name="typepad: what does SMP do"/> A 2007 publication in the ''[[Journal of Molecular Biology]]'' relied on multi-core processing to simulate the folding of part of the [[villin]] protein approximately 10 times longer than was possible with a single-processor client, in agreement with experimental folding rates.<ref name="10.1016/j.jmb.2007.09.069"/>

In November 2006, first-generation [[symmetric multiprocessing]] (SMP) clients were publicly released for open beta testing, referred to as SMP1.<ref name="High-Per FAQ"/> These clients used [[Message Passing Interface]] (MPI) communication protocols for parallel processing, as at that time the GROMACS cores were [[Thread-safe|not designed]] to be used with multiple threads.<ref name="SMP FAQ"/> This was the first time a distributed computing project had used MPI.<ref name="typepad: new client dev"/> Although the clients performed well in [[Unix]]-based operating systems such as Linux and macOS, they were troublesome under [[Microsoft Windows|Windows]].<ref name="typepad: what does SMP do"/><ref name="typepad: new client dev"/> On January&nbsp;24, 2010, SMP2, the second generation of the SMP clients and the successor to SMP1, was released as an open beta and replaced the complex MPI with a more reliable [[Thread (computer science)|thread]]-based implementation.<ref name="SMP2 release"/><ref name="typepad: how does dev get done"/>

SMP2 supports a trial of a special category of ''bigadv'' work units, designed to simulate proteins that are unusually large and computationally intensive and have a great scientific priority. These units originally required a minimum of eight CPU cores,<ref name="bigadv"/> which was raised to sixteen later, on February&nbsp;7, 2012.<ref name="typepad: update on bigadv-16"/> Along with these added hardware requirements over standard SMP2 work units, they require more system resources such as [[random-access memory]] (RAM) and [[Internet bandwidth]]. In return, users who run these are rewarded with a 20% increase over SMP2's bonus point system.<ref name="typepad: bigadv points change"/> The bigadv category allows Folding@home to run especially demanding simulations for long times that had formerly required use of supercomputing [[Computer cluster#Compute clusters|clusters]] and could not be performed anywhere else on Folding@home.<ref name="bigadv"/> Many users with hardware able to run bigadv units have later had their hardware setup deemed ineligible for bigadv work units when CPU core minimums were increased, leaving them only able to run the normal SMP work units. This frustrated many users who invested significant amounts of money into the program only to have their hardware be obsolete for bigadv purposes shortly after. As a result, Pande announced in January 2014 that the bigadv program would end on January 31, 2015.<ref>{{cite web|url=https://foldingathome.org/home/revised-plans-for-bigadv-ba-experiment/ |title=Revised plans for BigAdv (BA) experiment |author=Vijay Pande |date=January 15, 2014 |access-date=October 6, 2014}}</ref>

==== V7 ====
[[File:F@h v7 novice shot.png|thumb|A sample image of the V7 client in Novice mode running under [[Windows&nbsp;7]]. In addition to a variety of controls and user details, V7 presents work unit information, such as its state, calculation progress, ETA, credit points, identification numbers, and description.]]

The V7 client is the seventh generation of the Folding@home client software, and is a full rewrite and unification of the prior clients for [[Microsoft Windows|Windows]], [[macOS]], and [[Linux]] operating systems.<ref name="V7 install guide"/><ref name="typepad: V7 in open beta"/> It was released on March&nbsp;22, 2012.<ref name="typepad: v7 rollout"/> Like its predecessors, V7 can run Folding@home in the background at a very low [[scheduling priority|priority]], allowing other applications to use CPU resources as they need. It is designed to make the installation, start-up, and operation more user-friendly for novices, and offer greater scientific flexibility to researchers than prior clients.<ref name="typepad: ATI core 16 released"/> V7 uses [[Trac]] for [[Bug tracking system|managing its bug tickets]] so that users can see its development process and provide feedback.<ref name="typepad: V7 in open beta"/>

V7 consists of four integrated elements. The user typically interacts with V7's open-source [[Graphical user interface|GUI]], named FAHControl.<ref name="FAHControl source code"/><ref name="Ticket #736"/> This has Novice, Advanced, and Expert user interface modes, and has the ability to monitor, configure, and control many remote folding clients from one computer. FAHControl directs FAHClient, a [[backend as a service|back-end]] application that in turn manages each FAHSlot (or ''slot''). Each slot acts as replacement for the formerly distinct Folding@home v6 uniprocessor, SMP, or GPU computer clients, as it can download, process, and upload work units independently. The FAHViewer function, modeled after the PS3's viewer, displays a real-time 3-D rendering, if available, of the protein currently being processed.<ref name="V7 install guide"/><ref name="typepad: V7 in open beta"/>

==== Google Chrome ====
In 2014, a client for the [[Google Chrome]] and [[Chromium (web browser)|Chromium]] web browsers was released, allowing users to run Folding@home in their web browser. The client used [[Google]]'s [[Native Client]] (NaCl) feature on Chromium-based web browsers to run the Folding@home code at near-native speed in a [[sandbox (computer security)|sandbox]] on the user's machine.<ref>{{cite web|last1=Pande|first1=Vijay|title=Adding a completely new way to fold, directly in the browser|url=https://foldingathome.org/home/adding-a-completely-new-way-to-fold-directly-in-the-browser/|website=foldingathome.org|publisher=Pande Lab, Stanford University|access-date=February 13, 2015|date=February 24, 2014}}</ref> Due to the phasing out of NaCL and changes at Folding@home, the web client was permanently shut down in June 2019.<ref>{{cite web |title=NaCL Web Client Shutdown Notice |url=http://nacl.foldingathome.org/ |website=Folding@Home |access-date=August 29, 2019 |archive-date=April 12, 2019 |archive-url=https://web.archive.org/web/20190412010651/http://nacl.foldingathome.org/ |url-status=dead }}</ref>

==== Android ====
In July 2015, a client for [[Android (operating system)|Android]] mobile phones was released on [[Google Play]] for devices running [[Android 4.4 KitKat]] or newer.<ref>{{cite web |first=Vijay |last=Pande |title=First full version of our Folding@Home client for Android Mobile phones |url=https://foldingathome.org/home/first-full-version-of-our-foldinghome-client-for-android-mobile-phones/ |work=Folding@Home |publisher=foldingathome.org |date=July 7, 2015 |access-date=May 31, 2016}}</ref><ref>{{cite web |title=Folding@Home |url=https://play.google.com/store/apps/details?id=com.sonymobile.androidapp.gridcomputing |work=[[Google Play]] |date=2016 |access-date=May 31, 2016}}</ref>

On February 16, 2018, the Android client, which was offered in cooperation with [[Sony Mobile|Sony]], was removed from Google Play. Plans were announced to offer an open source alternative in the future.<ref>{{Cite web|url=https://foldingathome.org/2018/02/02/android-client-overhaul/|title=Android client overhaul|date=February 2, 2018|website=Folding@home|language=en-US|access-date=July 22, 2019}}</ref>

== Comparison to other molecular simulators ==
[[Rosetta@home]] is a distributed computing project aimed at protein structure prediction and is one of the most accurate [[tertiary structure]] predictors.<ref name="10.1002/prot.21804"/><ref name="10.1002/prot.22210"/> The conformational states from Rosetta's software can be used to initialize a Markov state model as starting points for Folding@home simulations.<ref name="Simulation FAQ"/> Conversely, structure prediction algorithms can be improved from thermodynamic and kinetic models and the sampling aspects of protein folding simulations.<ref name="10.1371/journal.pone.0005840"/> As Rosetta only tries to predict the final folded state, and not how folding proceeds, Rosetta@home and Folding@home are complementary and address very different molecular questions.<ref name="Simulation FAQ"/><ref name="F@H vs R@h"/>

[[Anton (computer)|Anton]] is a special-purpose supercomputer built for molecular dynamics simulations. In October 2011, Anton and Folding@home were the two most powerful molecular dynamics systems.<ref name="typepad: comparison with Anton"/> Anton is unique in its ability to produce single ultra-long computationally costly molecular trajectories,<ref name="10.1021/ja207470h"/> such as one in 2010 which reached the millisecond range.<ref name="10.1145/1654059.1654099"/><ref name="10.1126/science.1187409"/> These long trajectories may be especially helpful for some types of biochemical problems.<ref name="10.1145/1364782.1364802"/><ref name="10.1146/annurev-biophys-042910-155245"/> However, Anton does not use Markov state models (MSM) for analysis. In 2011, the Pande lab constructed a MSM from two 100-[[microsecond|μs]] Anton simulations and found alternative folding pathways that were not visible through Anton's traditional analysis. They concluded that there was little difference between MSMs constructed from a limited number of long trajectories or one assembled from many shorter trajectories.<ref name="10.1021/ja207470h"/> In June 2011 Folding@home added sampling of an Anton simulation in an effort to better determine how its methods compare to Anton's.<ref name="forum: 7610/7611 in beta"/><ref name="description: 7610"/> However, unlike Folding@home's shorter trajectories, which are more amenable to distributed computing and other parallelizing methods, longer trajectories do not require adaptive sampling to sufficiently sample the protein's [[phase space]]. Due to this, it is possible that a combination of Anton's and Folding@home's simulation methods would provide a more thorough sampling of this space.<ref name="10.1021/ja207470h"/>

== See also ==
{{Portal|Biology|Medicine}}
{{Div col|colwidth=25em}}
* [[BOINC]]
* [[DreamLab]], for use on smartphones
* [[Foldit]]
* [[List of distributed computing projects]]
* [[Comparison of software for molecular mechanics modeling]]
* [[Molecular modeling on GPUs]]
* [[SETI@home]]
* [[Storage@home]]
* [[Molecule editor]]
* [[Volunteer computing]]
* [[World Community Grid]]
{{Div col end}}

== References ==
{{Reflist
| colwidth= 30em
| refs =

<!-- *** Books *** -->

<ref name="978-0-340-66316-5">{{cite book |last1= Collier |first1= Leslie |last2= Balows |first2= Albert |last3= Sussman |first3= Max |year= 1998 |title= Topley and Wilson's Microbiology and Microbial Infections |edition= ninth |volume= 1, ''Virology'' |editor1-last= Mahy |editor1-first= Brian |editor2-last= Collier |editor2-first= Leslie |publisher= Arnold |location= London |isbn= 978-0-340-66316-5 |pages= 75–91}}</ref>

<ref name="978-0-387-73905-2">{{cite book |title= Collagen: structure and mechanics |last= Fratzl |first= Peter |date= May 10, 2008 |publisher= Springer |isbn= 978-0-387-73905-2 |url= https://books.google.com/books?id=dyWFTqEtXXwC&pg=PA1 |access-date= March 17, 2012}}</ref>

<ref name="978-3-642-14389-2">{{cite book |author1=Travis Desell |author2=Anthony Waters |author3=Malik Magdon-Ismail |author4=Boleslaw K. Szymanski |author5=Carlos A. Varela |author6=Matthew Newby |author7=Heidi Newberg |author8=Andreas Przystawik |author9=David Anderson |chapter= Accelerating the MilkyWay@Home volunteer computing project with GPUs |title= 8th International Conference on Parallel Processing and Applied Mathematics (PPAM 2009) Part I |year= 2009 |pages= 276–288 |publisher=Springer |isbn= 978-3-642-14389-2|citeseerx=10.1.1.158.7614 }}</ref>

<ref name="978-1-58603-796-3">{{cite book |author1=A. Verma |author2=S.M. Gopal |author3=A. Schug |author4=J.S. Oh |author5=K.V. Klenin |author6=K.H. Lee |author7=W. Wenzel |chapter= Massively Parallel All Atom Protein Folding in a Single Day|publisher=IOS Press|series= Advances in Parallel Computing|title=Parallel Computing: Architectures Algorithms and Applications|editor1=C. Bischof|editor2=M. Brückner|editor3=P. Gibbon|editor4=G.R. Joubert|editor5=T. Lippert|editor6=B. Mohr|editor7=F. Peters|year= 2008 |volume= 15 |pages= 527–534 |issn= 0927-5452 |isbn= 978-1-58603-796-3}}</ref>

<!-- *** Publications (sorted by date) *** -->

<ref name="10.1126/science.1905840">{{cite journal |author1=M Hollstein |author2=D Sidransky |author3=B Vogelstein |author4=CC Harris |title= p53 mutations in human cancers |journal= Science |year= 1991 |volume= 253 |issue= 5015 |pages= 49–53 |doi= 10.1126/science.1905840 |pmid= 1905840 |bibcode= 1991Sci...253...49H|s2cid=38527914 |url=https://zenodo.org/record/1230948 }}</ref>

<ref name="10.1126/science.290.5498.1903">{{cite journal |author1=M. R. Shirts |author2=V. S. Pande. |s2cid=2854586 |title= Screen Savers of the World, Unite! |journal= Science |year= 2000 |volume= 290 |issue= 5498 |pages= 1903–1904 |doi= 10.1126/science.290.5498.1903 |pmid= 17742054}}</ref>

<ref name="10.1002/bip.10219">{{cite journal |author1=Vijay S. Pande |author2=Ian Baker |author3=Jarrod Chapman |author4=Sidney P. Elmer |author5=Siraj Khaliq |author6=Stefan M. Larson |author7=Young Min Rhee |author8=Michael R. Shirts |author9=Christopher D. Snow |author10=Eric J. Sorin |author11=Bojan Zagrovic |title= Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing |journal= Biopolymers |year= 2002 |volume= 68 |issue= 1 |pages= 91–109 |doi= 10.1002/bip.10219 |pmid= 12579582}}</ref>

<ref name="10.1038/nature01160">{{cite journal |author1= Christopher D. Snow |author2= Houbi Nguyen |author3= Vijay S. Pande |author4= Martin Gruebele |title= Absolute comparison of simulated and experimental protein-folding dynamics |journal= Nature |year= 2002 |volume= 420 |issue= 6911 |pages= 102–106 |doi= 10.1038/nature01160 |pmid= 12422224 |url= http://sansan.phy.ncu.edu.tw/~hclee/ref/SnowNature2002.pdf |archive-url= https://web.archive.org/web/20120324051529/http://sansan.phy.ncu.edu.tw/~hclee/ref/SnowNature2002.pdf |url-status= dead |archive-date= March 24, 2012 |bibcode= 2002Natur.420..102S |s2cid= 1061159 }}</ref>

<ref name="10.1038/nature02265">{{cite journal |author1=Fred E. Cohen |author2=Jeffery W. Kelly |title= Therapeutic approaches to protein misfolding diseases |type= review |journal= Nature |year= 2003 |volume= 426 |issue= 6968 |pages= 905–9 |doi= 10.1038/nature02265 |pmid= 14685252|bibcode= 2003Natur.426..905C|s2cid=4421600 }}</ref>

<ref name="10.1016/j.jmb.2004.10.083">{{cite journal |author1=L. T. Chong |author2=C. D. Snow |author3=Y. M. Rhee |author4=V. S. Pande. |title= Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations |journal= Journal of Molecular Biology |year= 2004 |volume= 345 |issue= 4 |pages= 869–878 |doi= 10.1016/j.jmb.2004.10.083 |pmid= 15588832|citeseerx=10.1.1.132.1174 }}</ref>

<ref name="10.1016/S0140-6736(04)16051-0">{{cite journal |vauthors=Rauch F, Glorieux FH |title= Osteogenesis imperfecta |journal= Lancet |year= 2004 |pages= 1377–85 |volume= 363 |issue= 9418 |pmid= 15110498 |doi= 10.1016/S0140-6736(04)16051-0|s2cid= 24081895 }}</ref>

<ref name="10.1038/sj.embor.7400108">{{cite journal |author= Caroline Hadley |title= Biologists think bigger |journal= EMBO Reports |year= 2004 |volume= 5 |issue= 3 |pages= 236–238 |doi= 10.1038/sj.embor.7400108 |pmid=14993921 |pmc=1299019}}</ref>

<ref name="10.1016/j.jmb.2005.12.083">{{cite journal |author1=Lillian T. Chong |author2=William C. Swope |author3=Jed W. Pitera |author4=Vijay S. Pande |title= Kinetic Computational Alanine Scanning: Application to p53 Oligomerization |journal= Journal of Molecular Biology |year= 2005 |volume= 357 |issue= 3 |pages= 1039–1049 |doi= 10.1016/j.jmb.2005.12.083 |pmid= 16457841|s2cid=16156007 }}</ref>

<ref name="10.1002/jcc.20301">{{cite journal |author1=Sanghyun Park |author2=Randall J. Radmer |author3=Teri E. Klein |author4=Vijay S. Pande |title= A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides |journal= Journal of Computational Chemistry |year= 2005 |volume= 26 |issue= 15 |pages= 1612–1616 |doi= 10.1002/jcc.20301 |pmid= 16170799|citeseerx=10.1.1.142.6781 |s2cid=13051327 }}</ref>

<ref name="10.1146/annurev.biophys.34.040204.144447">{{cite journal |author1=C. D. Snow |author2=E. J. Sorin |author3=Y. M. Rhee |author4=V. S. Pande. |title= How well can simulation predict protein folding kinetics and thermodynamics? |type= review |journal= Annual Review of Biophysics |year= 2005 |volume= 34 |pages= 43–69 |doi= 10.1146/annurev.biophys.34.040204.144447 |pmid= 15869383}}</ref>

<ref name="10.1126/science.309.5731.78b">{{cite journal |title= So Much More to Know |journal= Science |year= 2005 |volume= 309 |issue= 5731 |pages= 78–102 |doi= 10.1126/science.309.5731.78b |pmid= 15994524 |s2cid= 33234834}}</ref>

<ref name="10.1063/1.2221680">{{cite journal |author1=Guha Jayachandran |author2=M. R. Shirts |author3=S. Park |author4=V. S. Pande |title= Parallelized-Over-Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics |journal= Journal of Chemical Physics |year= 2006 |volume= 125 |issue= 8 |page= 084901 |doi= 10.1063/1.2221680 |pmid= 16965051 |bibcode= 2006JChPh.125h4901J}}</ref>

<ref name="10.1137/06065146X">{{cite journal|last=Chodera|first=John D.|author2=Swope, William C. |author3=Pitera, Jed W. |author4= Dill, Ken A. |title=Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations|journal=Multiscale Modeling & Simulation|date=January 1, 2006|volume=5|issue=4|pages=1214–1226|doi=10.1137/06065146X|s2cid=17825277 |url=http://www.escholarship.org/uc/item/92q5z171}}</ref>

<ref name="10.1002/prot.21804">{{cite journal |vauthors=Lensink MF, Méndez R, Wodak SJ |title= Docking and scoring protein complexes: CAPRI 3rd Edition |journal= Proteins |volume= 69 |issue= 4 |pages= 704–18 |date=December 2007 |pmid= 17918726 |doi= 10.1002/prot.21804|s2cid= 25383642 }}</ref>

<ref name="10.1073/pnas.0608256104">{{cite journal |author1=Del Lucent |author2=V. Vishal |author3=Vijay S. Pande |title= Protein folding under confinement: A role for solvent |journal= [[Proceedings of the National Academy of Sciences of the United States of America]] |year= 2007 |volume= 104 |issue= 25 |pages= 10430–10434 |doi= 10.1073/pnas.0608256104 |pmid=17563390 |bibcode= 2007PNAS..10410430L|pmc= 1965530 |doi-access=free }}</ref>

<ref name="10.1016/S0140-6736(07)60111-1">{{cite journal |author= Walker FO |title= Huntington's disease |journal= Lancet |volume= 369 |issue= 9557 |year= 2007 |pmid= 17240289 |doi= 10.1016/S0140-6736(07)60111-1 |pages= 218–28 [220]|s2cid= 46151626 }}</ref>

<ref name="10.1111/j.1467-8659.2007.01012.x">{{cite journal |author1=John D. Owens |author2=David Luebke |author3=Naga Govindaraju |author4=Mark Harris |author5=Jens Krüger |author6=Aaron Lefohn |author7=Timothy J. Purcell |title= A Survey of General-Purpose Computation on Graphics Hardware |journal= Computer Graphics Forum |year= 2007 |volume= 26 |issue= 1 |pages= 80–113 |doi= 10.1111/j.1467-8659.2007.01012.x|citeseerx=10.1.1.215.426 |s2cid=62756490 }}</ref>

<ref name="10.1016/j.jmb.2007.09.069">{{cite journal |author1=Daniel L. Ensign |author2=Peter M. Kasson |author3=Vijay S. Pande |title= Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece |journal= Journal of Molecular Biology |year= 2007 |volume= 374 |issue= 3 |pages= 806–816 |doi= 10.1016/j.jmb.2007.09.069 |pmid= 17950314|pmc=3689540 }}</ref>

<ref name="10.1093/bioinformatics/btm250">{{cite journal |author1=Peter M. Kasson |author2=Afra Zomorodian |author3=Sanghyun Park |author4=Nina Singhal |author5=Leonidas J. Guibas |author6=Vijay S. Pande |title= Persistent voids: a new structural metric for membrane fusion |journal= Bioinformatics |year= 2007 |volume= 23 |issue= 14 |pages= 1753–1759 |doi= 10.1093/bioinformatics/btm250 |pmid= 17488753|doi-access= free }}</ref>

<ref name="10.1002/jcc.20703">{{cite journal |author1=Carsten Kutzner |author2=David Van Der Spoel |author3=Martin Fechner |author4=Erik Lindahl |author5=Udo W. Schmitt |author6=Bert L. De Groot |author7=Helmut Grubmüller |title= Speeding up parallel GROMACS on high-latency networks |journal= Journal of Computational Chemistry |year= 2007 |volume= 28 |issue= 12 |pages= 2075–2084 |doi= 10.1002/jcc.20703 |pmid= 17405124|hdl=11858/00-001M-0000-0012-E29A-0 |s2cid=519769 |hdl-access=free }}</ref>

<ref name="10.2119/2007-00100.Irvine">{{cite journal |author1=G Brent Irvine |author2=Omar M El-Agnaf |author3=Ganesh M Shankar |author4=Dominic M Walsh |title= Protein Aggregation in the Brain: The Molecular Basis for Alzheimer's and Parkinson's Diseases |journal= Molecular Medicine |type= review |volume= 14 |issue= 7–8 |pages= 451–464 |year= 2008 |pmid= 18368143 |doi= 10.2119/2007-00100.Irvine |pmc= 2274891}}</ref>

<ref name="10.1145/1364782.1364802">{{cite journal |author1= David E. Shaw |author2=Martin M. Deneroff |author3=Ron O. Dror |author4=Jeffrey S. Kuskin |author5=Richard H. Larson |author6=John K. Salmon |author7=Cliff Young |author8=Brannon Batson |author9=Kevin J. Bowers |author10=Jack C. Chao |author11=Michael P. Eastwood |author12=Joseph Gagliardo |author13=J. P. Grossman |author14=C. Richard Ho |author15=Douglas J. Ierardi |display-authors=etal |title= Anton, A Special-Purpose Machine for Molecular Dynamics Simulation |journal= Communications of the ACM |volume= 51 |issue= 7 |pages= 91–97 |year= 2008 |doi= 10.1145/1364782.1364802 |doi-access=free }}</ref>

<ref name="10.1016/j.abb.2007.05.014">{{cite journal |author1=Yiwen Chen |author2=Feng Ding |author3=Huifen Nie |author4=Adrian W. Serohijos |author5=Shantanu Sharma |author6=Kyle C. Wilcox |author7=Shuangye Yin |author8=Nikolay V. Dokholyan |title= Protein folding: Then and now |journal= Archives of Biochemistry and Biophysics |year= 2008 |volume= 469 |issue= 1 |pages= 4–19 |doi= 10.1016/j.abb.2007.05.014 |pmc= 2173875 |pmid= 17585870}}</ref>

<ref name="10.1021/ct700301q">{{cite journal |author1=Berk Hess |author2=Carsten Kutzner |author3=David van der Spoel |author4=Erik Lindahl |title= GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation |journal= Journal of Chemical Theory and Computation |year= 2008 |volume= 4 |issue= 3 |pages= 435–447 |doi= 10.1021/ct700301q|pmid=26620784 |hdl= 11858/00-001M-0000-0012-DDBF-0 |s2cid=1142192 |hdl-access= free }}</ref>

<ref name="10.1002/iub.117">{{cite journal |author1=Heath Ecroyd |author2=John A. Carver |title= Unraveling the mysteries of protein folding and misfolding |type= review |journal= IUBMB Life |year= 2008 |volume= 60 |issue= 12 |pages= 769–774 |doi= 10.1002/iub.117 |pmid =18767168|s2cid=10115925 |url= https://ro.uow.edu.au/cgi/viewcontent.cgi?article=1968&context=scipapers |doi-access= free }}</ref>

<ref name="10.1073/pnas.0801795105">{{cite journal |author1=Paula M. Petrone |author2=Christopher D. Snow |author3=Del Lucent |author4=Vijay S. Pande |title= Side-chain recognition and gating in the ribosome exit tunnel |journal= Proceedings of the National Academy of Sciences |year= 2008 |volume= 105 |issue= 43 |pages=16549–54 |doi= 10.1073/pnas.0801795105 |bibcode= 2008PNAS..10516549P |pmid=18946046 |pmc=2575457|doi-access=free }}</ref>

<ref name="10.1002/jcc.21054">{{cite journal |author1=Edgar Luttmann |author2=Daniel L. Ensign |author3=Vishal Vaidyanathan |author4=Mike Houston |author5=Noam Rimon |author6=Jeppe Øland |author7=Guha Jayachandran |author8=Mark Friedrichs |author9=Vijay S. Pande |title= Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3 |journal= Journal of Computational Chemistry |year= 2008 |volume= 30 |issue= 2 |pages= 268–274 |doi= 10.1002/jcc.21054 |pmid= 18615421|s2cid=33047431 |doi-access=free }}</ref>

<ref name="10.1016/j.cbpa.2008.02.011">{{cite journal |author1=Leila M Luheshi |author2=Damian Crowther |author3=Christopher Dobson |title= Protein misfolding and disease: from the test tube to the organism |journal= Current Opinion in Chemical Biology |year= 2008 |volume= 12 |issue= 1 |pages= 25–31 |doi= 10.1016/j.cbpa.2008.02.011 |pmid= 18295611}}</ref>

<ref name="10.1001/archneurol.2007.56">{{cite journal |author1=Claudio Soto |author2=Lisbell D. Estrada |title= Protein Misfolding and Neurodegeneration |type= review |journal= Archives of Neurology |year= 2008 |volume= 65 |issue= 2 |pages= 184–189 |doi= 10.1001/archneurol.2007.56 |pmid= 18268186|doi-access=  }}</ref>

<ref name="10.1074/jbc.R800036200">{{cite journal |author1=Robin Roychaudhuri |author2=Mingfeng Yang |author3=Minako M. Hoshi |author4=David B. Teplow |title= Amyloid β-Protein Assembly and Alzheimer Disease |journal= Journal of Biological Chemistry |year= 2008 |volume= 284 |issue= 8 |pages= 4749–53 |doi= 10.1074/jbc.R800036200 |pmid= 18845536|pmc=3837440 |doi-access=free }}</ref>

<ref name="10.1063/1.3010881">{{cite journal |author1=Nicholas W. Kelley |author2=V. Vishal |author3=Grant A. Krafft |author4=Vijay S. Pande. |title= Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach |journal= Journal of Chemical Physics |year= 2008 |volume= 129 |issue= 21 |page= 214707 |doi= 10.1063/1.3010881 |pmid= 19063575 |pmc= 2674793 |bibcode= 2008JChPh.129u4707K}}</ref>

<ref name="10.1002/prot.22210">{{cite journal |author1=Gregory R. Bowman |author2=Vijay S. Pande |title= Simulated tempering yields insight into the low-resolution Rosetta scoring function |journal= Proteins: Structure, Function, and Bioinformatics |year= 2009 |volume= 74 |issue= 3 |pages= 777–88 |doi= 10.1002/prot.22210 |pmid= 18767152|s2cid=29895006 }}</ref>

<ref name="10.1016/j.bpj.2009.04.059">{{cite journal |vauthors=Gautieri A, Uzel S, Vesentini S, Redaelli A, Buehler MJ |title= Molecular and mesoscale disease mechanisms of Osteogenesis Imperfecta |journal= Biophysical Journal |year= 2009 |pages= 857–865 |volume= 97 |issue= 3 |pmid= 19651044 |doi= 10.1016/j.bpj.2009.04.059 |pmc= 2718154 |bibcode= 2009BpJ....97..857G}}</ref>

<ref name="10.1021/ja904557w">{{cite journal |author1=Peter M. Kasson |author2=Daniel L. Ensign |author3=Vijay S. Pande |title= Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin |journal= Journal of the American Chemical Society |year= 2009 |volume= 131 |issue= 32 |pages= 11338–11340 |doi= 10.1021/ja904557w |pmid= 19637916 |pmc= 2737089|bibcode=2009JAChS.13111338K }}</ref>

<ref name="19209725, 2811693">{{cite journal |author1=Peter M. Kasson |author2=Vijay S. Pande |title= Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin |journal= Pacific Symposium on Biocomputing |year= 2009 |pages= 492–503 |pmid= 19209725 |pmc= 2811693|doi=10.1142/9789812836939_0047 |isbn=978-981-283-692-2 }}</ref>

<ref name="10.1371/journal.pone.0005840">{{cite journal |author1=G. R. Bowman |author2=V. S. Pande |title= The Roles of Entropy and Kinetics in Structure Prediction |journal= PLOS ONE |year= 2009 |volume= 4 |issue= 6 |pages= e5840 |doi= 10.1371/journal.pone.0005840 |pmid= 19513117 |pmc= 2688754 |bibcode= 2009PLoSO...4.5840B |editor1-last= Hofmann |editor1-first= Andreas|doi-access= free }}</ref>

<ref name="10.1145/1654059.1654099">{{cite book |author= David E. Shaw |title= Proceedings of the Conference on High Performance Computing Networking, Storage and Analysis - SC '09 |year= 2009 |issue= 39 |pages= 1–11 |doi= 10.1145/1654059.1654099 |isbn= 978-1-60558-744-8 |display-authors= 1 |last2= Bowers |first2= Kevin J. |last3= Chow |first3= Edmond |last4= Eastwood |first4= Michael P. |last5= Ierardi |first5= Douglas J. |last6= Klepeis |first6= John L. |last7= Kuskin |first7= Jeffrey S. |last8= Larson |first8= Richard H. |last9= Lindorff-Larsen |first9= Kresten|chapter= Millisecond-scale molecular dynamics simulations on Anton |s2cid= 53234452 }}</ref>

<ref name="10.1093/bib/bbp023">{{cite journal |author1=Chun Song |author2=Shen Lim |author3=Joo Tong |title= Recent advances in computer-aided drug design |type= review |journal= Briefings in Bioinformatics |year= 2009 |volume= 10 |issue= 5 |pages= 579–91 |doi= 10.1093/bib/bbp023 |pmid= 19433475|doi-access= free }}</ref>

<ref name="10.1002/jcc.21209">{{cite journal |author1=M. S. Friedrichs |author2=P. Eastman |author3=V. Vaidyanathan |author4=M. Houston |author5=S. LeGrand |author6=A. L. Beberg |author7=D. L. Ensign |author8=C. M. Bruns |author9=V. S. Pande |title= Accelerating Molecular Dynamic Simulation on Graphics Processing Units |journal= Journal of Computational Chemistry |year= 2009 |volume= 30 |issue= 6 |pages= 864–72 |doi= 10.1002/jcc.21209 |pmid= 19191337 |pmc= 2724265}}</ref>

<ref name="10.1109/IPDPS.2009.5160922">{{cite book |author1=Adam Beberg |author2=Daniel Ensign |author3=Guha Jayachandran |author4=Siraj Khaliq |author5=Vijay Pande |chapter= Folding@home: Lessons from eight years of volunteer distributed computing|title= 2009 IEEE International Symposium on Parallel & Distributed Processing|year= 2009 |pages= 1–8 |doi= 10.1109/IPDPS.2009.5160922 |issn= 1530-2075 |chapter-url= http://www.hicomb.org/papers/HICOMB2009-13.pdf |isbn= 978-1-4244-3751-1|s2cid=15677970 }}</ref>

<ref name="10.1371/journal.pcbi.1000452">{{cite journal |author1=Fabrizio Marinelli |author2=Fabio Pietrucci |author3=Alessandro Laio |author4=Stefano Piana |title= A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations |journal= PLOS Computational Biology |year= 2009 |volume= 5 |issue= 8 |pages= e1000452 |doi= 10.1371/journal.pcbi.1000452 |editor1-first= Vijay S. |editor1-last= Pande|bibcode= 2009PLSCB...5E0452M |pmid=19662155 |pmc=2711228 |doi-access= free }}</ref>

<ref name="Protein Misfolding Diseases">{{cite journal|author1=Vittorio Bellotti |author2=Monica Stoppini |title=Protein Misfolding Diseases |journal=The Open Biology Journal |year=2009 |volume=2 |issue=2 |pages=228–234 |url=http://www.benthamscience.com/open/tobioj/articles/V002/SI0161TOBIOJ/228TOBIOJ.pdf |doi=10.2174/1874196700902020228 |doi-broken-date=November 1, 2024 |url-status=deviated |archive-url=https://web.archive.org/web/20140222042205/http://www.benthamscience.com/open/tobioj/articles/V002/SI0161TOBIOJ/228TOBIOJ.pdf |archive-date=February 22, 2014  }}</ref>

<ref name="10.1016/j.jmb.2009.01.032">{{cite journal |author1=Nicholas W. Kelley |author2=Xuhui Huang |author3=Stephen Tam |author4=Christoph Spiess |author5=Judith Frydman |author6=Vijay S. Pande |title= The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation |journal= Journal of Molecular Biology |year= 2009 |volume= 388 |issue= 5 |pages= 919–27 |doi= 10.1016/j.jmb.2009.01.032 |pmid= 19361448 |pmc= 2677131}}</ref>

<ref name="10.3390/ijms11125292">{{cite journal |author1=Timothy H. Click |author2=Debabani Ganguly |author3=Jianhan Chen |title= Intrinsically Disordered Proteins in a Physics-Based World |journal= International Journal of Molecular Sciences |year= 2010 |volume= 11 |issue= 12 |pages= 919–27 |doi= 10.3390/ijms11125292 |pmid= 21614208 |pmc= 3100817|doi-access=free }}</ref>

<ref name="10.1126/science.1187409">{{cite journal |author= David E. Shaw |title= Atomic-Level Characterization of the Structural Dynamics of Proteins |journal= Science |year= 2010 |volume= 330 |issue= 6002 |pages= 341–346 |doi= 10.1126/science.1187409 |pmid= 20947758 |bibcode= 2010Sci...330..341S| display-authors= 1 |last2= Maragakis |first2= P. |last3= Lindorff-Larsen |first3= K. |last4= Piana |first4= S. |last5= Dror |first5= R. O. |last6= Eastwood |first6= M. P. |last7= Bank |first7= J. A. |last8= Jumper |first8= J. M. |last9= Salmon |first9= J. K.|s2cid= 3495023 }}</ref>

<ref name="10.1073/pnas.1003962107">{{cite journal |author1=Gregory R. Bowman |author2=Vijay S. Pande |title= Protein folded states are kinetic hubs |journal= Proceedings of the National Academy of Sciences |year= 2010 |volume= 107 |issue= 24 |pages=10890–5 |doi= 10.1073/pnas.1003962107 |bibcode= 2010PNAS..10710890B |pmid=20534497 |pmc=2890711|doi-access=free }}</ref>

<ref name="10.1021/ja908369h">{{cite journal |author1=Vincent A. Voelz |author2=Vijay R. Singh |author3=William J. Wedemeyer |author4=Lisa J. Lapidus |author5=Vijay S. Pande |title= Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment |journal= Journal of the American Chemical Society |year= 2010 |volume= 132 |issue= 13 |pages= 4702–4709 |doi= 10.1021/ja908369h |pmid= 20218718 |pmc= 2853762|bibcode=2010JAChS.132.4702V }}</ref>

<ref name="10.1109/CCGRID.2010.84">{{cite book |author1=I. Haque |author2=V. S. Pande |chapter= Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU|title= 2010 10th IEEE/ACM International Conference on Cluster, Cloud and Grid Computing|year= 2010 |pages= 691–696 |doi= 10.1109/CCGRID.2010.84 |isbn= 978-1-4244-6987-1|arxiv= 0910.0505 |s2cid=10723933 }}</ref>

<ref name="10.1021/ja9090353">{{cite journal |author1=Vincent A. Voelz |author2=Gregory R. Bowman |author3=Kyle Beauchamp |author4=Vijay S. Pande |title= Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1–39) |journal= Journal of the American Chemical Society |year= 2010 |volume= 132 |issue= 5 |pages= 1526–1528 |doi= 10.1021/ja9090353 |pmid= 20070076 |pmc= 2835335}}</ref>

<ref name="10.1109/MCSE.2010.27">{{cite journal |author1=P. Eastman |author2=V. S. Pande |title= OpenMM: A Hardware-Independent Framework for Molecular Simulations |journal= Computing in Science and Engineering |year= 2010 |volume= 12 |issue= 4 |pages= 34–39 |doi= 10.1109/MCSE.2010.27 |pmid=26146490 |pmc=4486654 |issn= 1521-9615|bibcode=2010CSE....12d..34E }}</ref>

<ref name="10.1038/nchembio.279">{{cite journal |author1=Susan W Liebman |author2=Stephen C Meredith |title= Protein folding: Sticky N17 speeds huntingtin pile-up |journal= Nature Chemical Biology |year= 2010 |volume= 6 |issue= 1 |pages= 7–8 |doi= 10.1038/nchembio.279 |pmid= 20016493}}</ref>

<ref name="10.1021/ct900620b">{{cite journal |author1=Gregory R. Bowman |author2=Daniel L. Ensign |author3=Vijay S. Pande |title= Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models |journal= Journal of Chemical Theory and Computation |year= 2010 |volume= 6 |issue= 3 |pages= 787–794 |doi= 10.1021/ct900620b|pmid=23626502 |pmc=3637129 }}</ref>

<ref name="10.1016/j.ymeth.2010.06.002">{{cite journal |author1=V. S. Pande |author2=K. Beauchamp |author3=G. R. Bowman |title= Everything you wanted to know about Markov State Models but were afraid to ask |journal= Methods |year= 2010 |volume= 52 |issue= 1 |pages= 99–105 |doi= 10.1016/j.ymeth.2010.06.002 |pmc= 2933958 |pmid= 20570730}}</ref>

<ref name="10.1038/cr.2010.57">{{cite journal |author1=Gregory R Bowman |author2=Xuhui Huang |author3=Vijay S Pande |title= Network models for molecular kinetics and their initial applications to human health |type= review |journal= Cell Research |year= 2010 |volume= 20 |issue= 6 |pages= 622–630 |doi= 10.1038/cr.2010.57 |pmid= 20421891|pmc=4441225 }}</ref>

<ref name="10.1073/pnas.1010880108">{{cite journal |author1=Kyle A. Beauchamp |author2=Daniel L. Ensign |author3=Rhiju Das |author4=Vijay S. Pande |title= Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments |journal= Proceedings of the National Academy of Sciences |year= 2011 |volume= 108 |issue= 31 |pages=12734–9 |doi= 10.1073/pnas.1010880108 |bibcode= 2011PNAS..10812734B |pmid=21768345 |pmc=3150881|doi-access=free }}</ref>

<ref name="Pronk et al, 2011">{{Cite book |last1=Pronk |first1=Sander |last2=Larsson |first2=Per |last3=Pouya |first3=Iman |last4=Bowman |first4=Gregory R. |last5=Haque |first5=Imran S. |last6=Beauchamp |first6=Kyle |last7=Hess |first7=Berk |last8=Pande |first8=Vijay S. |last9=Kasson |first9=Peter M. |last10=Lindahl |first10=Erik |chapter=Copernicus: A new paradigm for parallel adaptive molecular dynamics |date=2011-11-12 |title=Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis |chapter-url=https://dl.acm.org/doi/10.1145/2063384.2063465 |language=en |publisher=ACM |pages=1–10 |doi=10.1145/2063384.2063465 |isbn=978-1-4503-0771-0}}</ref>

<ref name="10.1039/c0cs00115e">{{cite journal |author1=Hana Robson Marsden |author2=Itsuro Tomatsu |author3=Alexander Kros |title= Model systems for membrane fusion |type= review |journal= Chemical Society Reviews |year= 2011 |volume= 40 |issue= 3 |pages= 1572–1585 |doi= 10.1039/c0cs00115e |pmid= 21152599}}</ref>

<ref name="10.1007/s12013-011-9200-x">{{cite journal |author1=Aabgeena Naeem |author2=Naveed Ahmad Fazili |title= Defective Protein Folding and Aggregation as the Basis of Neurodegenerative Diseases: The Darker Aspect of Proteins |type= review |journal= [[Cell Biochemistry and Biophysics]] |year= 2011 |volume= 61 |issue= 2 |pages= 237–50 |doi= 10.1007/s12013-011-9200-x |pmid= 21573992|s2cid=22622999 }}</ref>

<ref name="10.1016/j.sbi.2010.10.006">{{cite journal |author1=G. Bowman |author2=V. Volez |author3=V. S. Pande |title= Taming the complexity of protein folding |journal= Current Opinion in Structural Biology |year= 2011 |volume= 21 |issue= 1 |pages= 4–11 |doi= 10.1016/j.sbi.2010.10.006 |pmc= 3042729 |pmid= 21081274}}</ref>

<ref name="10.1371/journal.pone.0021776">{{cite journal |author1= P. Novick |author2=J. Rajadas |author3=C.W. Liu |author4=N. W. Kelley |author5=M. Inayathullah |author6=V. S. Pande |title= Rationally Designed Turn Promoting Mutation in the Amyloid-β Peptide Sequence Stabilizes Oligomers in Solution |journal= PLOS ONE |year= 2011 |volume= 6 |issue= 7 |pages= e21776 |doi= 10.1371/journal.pone.0021776 |pmc= 3142112 |pmid= 21799748 |editor1-last= Buehler |editor1-first= Markus J.|bibcode= 2011PLoSO...621776R|doi-access= free }}</ref>

<ref name="10.1021/ja207470h">{{cite journal |author1=Thomas J. Lane |author2=Gregory R. Bowman |author3=Kyle A Beauchamp |author4=Vincent Alvin Voelz |author5=Vijay S. Pande |title= Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories |journal= Journal of the American Chemical Society |year= 2011 |volume= 133 |issue= 45 |pages= 18413–9 |doi= 10.1021/ja207470h |pmid= 21988563 |pmc= 3227799|bibcode=2011JAChS.13318413L }}</ref>

<ref name="10.1039/C1CP22100K">{{cite journal |author1=Phineus R. L. Markwick |author2=J. Andrew McCammon |title= Studying functional dynamics in bio-molecules using accelerated molecular dynamics |journal=  Physical Chemistry Chemical Physics |year= 2011 |volume= 13 |issue= 45 |pages= 20053–65 |doi= 10.1039/C1CP22100K |pmid= 22015376 |bibcode= 2011PCCP...1320053M}}</ref>

<ref name="10.1016/j.biopha.2011.04.025">{{cite journal |vauthors=Almeida MB, do Nascimento JL, Herculano AM, Crespo-López ME |title= Molecular chaperones: toward new therapeutic tools |type= review |journal= Journal of Molecular Biology |year= 2011 |volume= 65 |issue= 4 |pages= 239–43 |doi= 10.1016/j.biopha.2011.04.025 |pmid= 21737228}}</ref>

<ref name="10.1016/j.sbi.2011.12.001">{{cite journal |author= Robert B Best |title= Atomistic molecular simulations of protein folding |journal= Current Opinion in Structural Biology |year= 2012 |type= review |volume= 22 |issue= 1 |pages= 52–61 |doi= 10.1016/j.sbi.2011.12.001 |pmid= 22257762}}</ref>

<ref name="10.1021/jm201332p">{{cite journal |author1=Paul A. Novick |author2=Dahabada H. Lopes |author3=Kim M. Branson |author4=Alexandra Esteras-Chopo |author5=Isabella A. Graef |author6=Gal Bitan |author7=Vijay S. Pande |title= Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif |journal= Journal of Medicinal Chemistry |year= 2012 |volume= 55 |issue= 7 |pages= 3002–10 |doi= 10.1021/jm201332p |pmid= 22420626|pmc=3766731 }}</ref>

<ref name="10.1038/nature10975">{{cite journal |author1=Aron M. Levin |author2=Darren L. Bates |author3=Aaron M. Ring |author4=Carsten Krieg |author5=Jack T. Lin |author6=Leon Su |author7=Ignacio Moraga |author8=Miro E. Raeber |author9=Gregory R. Bowman |author10=Paul Novick |author11=Vijay S. Pande |author12=C. Garrison Fathman |author13=Onur Boyman |author14=K. Christopher Garcia |title= Exploiting a natural conformational switch to engineer an interleukin-2 'superkine' |journal= Nature |year= 2012 |volume= 484 |issue= 7395 |pages= 529–33 |doi= 10.1038/nature10975 |pmid= 22446627 |pmc= 3338870 |bibcode= 2012Natur.484..529L}}</ref>

<ref name="10.1073/pnas.1209309109">{{cite journal |title= Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites |author1=Gregory R. Bowman |author2=Phillip L. Geissler |journal= [[PNAS]] |date=July 2012 |volume= 109 |issue= 29 |pages=11681–6 |doi= 10.1073/pnas.1209309109 |pmid=22753506 |pmc=3406870 |bibcode= 2012PNAS..10911681B|doi-access=free }}</ref>

<ref name="10.1146/annurev-biophys-042910-155245">{{cite journal |title= Biomolecular Simulation: A Computational Microscope for Molecular Biology |author1=Ron O. Dror |author2=Robert M. Dirks |author3=J.P. Grossman |author4=Huafeng Xu |author5=David E. Shaw |journal= [[Annual Review of Biophysics]] |year= 2012 |volume= 41 |pages= 429–52 |doi= 10.1146/annurev-biophys-042910-155245 |pmid=22577825 }}</ref>

<ref name="10.1016/j.cub.2012.01.008">{{cite journal |author= Michael Gross |title= Folding research recruits unconventional help |journal= Current Biology |year= 2012 |volume= 22 |issue= 2 |pages= R35–R38 |doi= 10.1016/j.cub.2012.01.008 |pmid= 22389910|doi-access= free |bibcode= 2012CBio...22..R35G }}</ref>

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<ref name="About Partners">{{cite web |url=https://foldingathome.org/about/partners/ |title=About Folding@home Partners |author=foldingathome.org |date=September 27, 2016 |access-date=September 2, 2019 |archive-date=April 23, 2020 |archive-url=https://web.archive.org/web/20200423092734/https://foldingathome.org/about/partners/ |url-status=dead }}</ref>

<ref name="papers">{{cite web|url=https://foldingathome.org/papers-results/ |title=Papers & Results from Folding@home |author=Pande lab |work=Folding@home |publisher=foldingathome.org |date=July 27, 2012 |access-date= February 1, 2019 |archive-url=https://web.archive.org/web/20120717062813/http://folding.stanford.edu/English/Papers |archive-date=July 17, 2012 |url-status=live }}</ref>

<ref name="Open Source FAQ">{{cite web |url=https://foldingathome.org/support/faq/opensource/ |title=Folding@home Open Source FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 2, 2012 |access-date=July 8, 2013 |archive-url = https://web.archive.org/web/20200303094636/https://foldingathome.org/support/faq/opensource/ |archive-date = March 3, 2020  }}</ref>

<ref name="Simulation FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-simulation/ |title=Folding@home Simulation FAQ |author1=TJ Lane |author2=Gregory Bowman |author3=Robert McGibbon |author4=Christian Schwantes |author5=Vijay Pande |author6=Bruce Borden |work=Folding@home |publisher=foldingathome.org |date=September 10, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120913150805/http://folding.stanford.edu/English/FAQ-Simulation |archive-date=September 13, 2012 |url-status=dead  }}</ref>

<ref name="diseases FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-diseases/ |title=Folding@home Diseases Studied FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=May 30, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120825034819/http://folding.stanford.edu/English/FAQ-Diseases |archive-date=August 25, 2012 |url-status=dead  }}</ref>

<ref name="Press FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-press/ |title=Folding@Home Press FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |year=2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120825034819/http://folding.stanford.edu/English/FAQ-Diseases |archive-date=August 25, 2012 |url-status=dead  }}</ref>

<ref name="Main FAQ">{{cite web|url=https://foldingathome.org/home/faq/ |title=Folding@home Main FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 18, 2011 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20121120171555/http://folding.stanford.edu/English/FAQ-main |archive-date=November 20, 2012 |url-status=live  }}</ref>

<ref name="FAH osstats2">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats2 |title=Client Statistics by OS |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20150903080739/http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats2 |archive-date=September 3, 2015 |url-status=live  }}</ref>

<ref name="PS3 FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-ps3 |title=PS3 FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=May 30, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20130513144102/http://fah-web.stanford.edu/cgi-bin/main.py?qtype=osstats |archive-date=May 13, 2013 |url-status=dead  }}</ref>

<ref name="Points FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-points/ |title=Folding@home Points FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 20, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120717063319/http://folding.stanford.edu/English/FAQ-Points |archive-date=July 17, 2012 |url-status=dead  }}</ref>

<ref name="SMP FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-smp |title=Folding@home SMP FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=June 11, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120922013529/http://folding.stanford.edu/English/FAQ-SMP |archive-date=September 22, 2012 |url-status=dead  }}</ref>

<ref name="Uni Guide">{{cite web |url=https://foldingathome.org/home/guide/winuniguide |title=Windows Uniprocessor Client Installation Guide |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=Guide |date=February 10, 2011 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20121120201615/http://folding.stanford.edu/English/WinUNIGuide |archive-date=November 20, 2012 |url-status=dead  }}</ref>

<ref name="FAH license">{{cite web |url=https://foldingathome.org/home/License/ |title=Folding@home Distributed Computing Client |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120626201843/http://folding.stanford.edu/English/License |archive-date=June 26, 2012 |url-status=dead  }}</ref>

<ref name="Uninstall">{{cite web |url=https://foldingathome.org/home/guide/uninstall-guide |title=Uninstalling Folding@home Guide |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=Guide |date=May 30, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120717063427/http://folding.stanford.edu/English/FAQ-Uninstall |archive-date=July 17, 2012 |url-status=dead  }}</ref>

<ref name="High-Per FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-high-performance |title=High Performance FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=May 30, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120819053557/http://folding.stanford.edu/English/FAQ-highperformance |archive-date=August 19, 2012 |url-status=dead  }}</ref>

<ref name="ATI FAQ">{{cite web |url=https://foldingathome.org/English/FAQ-ATI |title=ATI FAQ |format=FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |date=March 18, 2011 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20121028125028/http://folding.stanford.edu/English/FAQ-ATI |archive-date=October 28, 2012 |url-status=dead  }}</ref>

<ref name="Executive summary">{{cite web|url=http://www.stanford.edu/group/pandegroup/folding/FoldingFAQ.pdf |title=Folding@Home Executive summary |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=October 4, 2011 |archive-url=https://web.archive.org/web/20121007155610/http://www.stanford.edu/group/pandegroup/folding/FoldingFAQ.pdf |archive-date=October 7, 2012 |url-status=live  }}</ref>

<ref name="V7 install guide">{{cite web |url=https://foldingathome.org/home/guide/windows-install-guide/ |title=Windows (FAH V7) Installation Guide |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=Guide |date=March 23, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20121028112953/http://folding.stanford.edu/English/WinGuide |archive-date=October 28, 2012 |url-status=dead  }}</ref>

<ref name="Petaflop FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-petaflop |title=Folding@home Petaflop Initiative |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 19, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120713024007/http://folding.stanford.edu/English/FAQ-Petaflop |archive-date=July 13, 2012 |url-status=dead  }}</ref>

<ref name="FAQ index">{{cite web |url=https://foldingathome.org/home/community-support/#faqs |title=Folding@home Frequently Asked Questions (FAQ) Index |author=Pande lab |work=Folding@home |publisher=foldingathome.org |date=August 7, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20121025165018/http://folding.stanford.edu/English/FAQ |archive-date=October 25, 2012 |url-status=dead  }}</ref>

<ref name="Gromacs FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-gromacs |title=Folding@home Gromacs FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 19, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120717063443/http://folding.stanford.edu/English/FAQ-gromacs |archive-date=July 17, 2012 |url-status=dead  }}</ref>

<ref name="Passkey FAQ">{{cite web |url=https://foldingathome.org/home/faq/faq-passkey/ |title=Folding@home Passkey FAQ |author=Pande lab |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=July 23, 2012 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120922051826/http://folding.stanford.edu/English/FAQ-passkey |archive-date=September 22, 2012 |url-status=dead  }}</ref>

<ref name="FAH Awards">{{cite web |url=https://foldingathome.org/home/awards |title=Folding@home&nbsp;– Awards |work=Folding@home |publisher=foldingathome.org |format=FAQ |date=August 2011 |access-date=July 8, 2013 |archive-url=https://web.archive.org/web/20120712133630/http://folding.stanford.edu/English/Awards |archive-date=July 12, 2012 |url-status=dead  }}</ref>

<ref name="Public client releases">{{cite web |url=https://download.foldingathome.org/releases/public/fah-client |access-date=February 15, 2025 |title=Index of /releases/public/fah-client/}}</ref>

<!-- *** Project descriptions (sorted numerically) *** -->

<ref name="description: 180">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=180 |title=Project 180 Description |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=September 27, 2011 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=180 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<ref name="description: 5765">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=5765 |title=Project 5765 Description |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=December 2, 2011 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=5765 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<ref name="description: 6571">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=6871 |title=Project 6871 Description |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=September 27, 2011 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=6871 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<ref name="description: 7600">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=7600 |title=Project 7600 Description |author=TJ Lane (Pande lab member) |work=Folding@home |publisher=foldingathome.org |date=June 8, 2011 |access-date=March 31, 2012 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=7600 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<ref name="description: 7610">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=7610 |title=Project 7610 Description |author=Pande lab |work=Folding@home |access-date=February 26, 2012 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=7610 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<ref name="description: 10721">{{cite web|url=http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=10721 |title=Project 10721 Description |author=Pande lab |work=Folding@home |publisher=foldingathome.org |access-date=September 27, 2011 |archive-url=https://web.archive.org/web/20160106095010/http://fah-web.stanford.edu/cgi-bin/fahproject.overusingIPswillbebanned?p=10721 |archive-date=January 6, 2016 |url-status=live  }}</ref>

<!-- *** Folding.typepad.edu pages (sorted by date) *** -->

<ref name="typepad: crossing 1 PF">{{cite web|url=http://folding.typepad.com/news/2007/09/crossing-the-pe.html |title=Crossing the petaFLOPS barrier |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=September 16, 2007 |access-date=August 28, 2011 |archive-url=https://web.archive.org/web/20120403123024/http://folding.typepad.com/news/2007/09/crossing-the-pe.html |archive-date=April 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: nanomedicine ce">{{cite web|url=http://folding.typepad.com/news/2007/09/nanomedicine-ce.html |title=Nanomedicine center |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=September 28, 2007 |access-date=September 23, 2011 |archive-url=https://web.archive.org/web/20121018232956/http://folding.typepad.com/news/2007/09/nanomedicine-ce.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: new client dev">{{cite web|url=http://folding.typepad.com/news/2008/03/new-windows-cli.html |title=New Windows client/core development (SMP and classic clients) |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=March 8, 2008 |access-date=September 30, 2011 |archive-url=https://web.archive.org/web/20121015011735/http://folding.typepad.com/news/2008/03/new-windows-cli.html |archive-date=October 15, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU2 open beta">{{cite web|url=http://folding.typepad.com/news/2008/04/gpu2-open-beta.html |title=GPU2 open beta |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 10, 2008 |access-date=September 7, 2011 |archive-url=https://archive.today/20120709022254/http://folding.typepad.com/news/2008/04/gpu2-open-beta.html |archive-date=July 9, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU2 going well">{{cite web|url=http://folding.typepad.com/news/2008/04/gpu2-open-bet-1.html |title=GPU2 open beta going well |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 11, 2008 |access-date=September 7, 2011 |archive-url=https://web.archive.org/web/20120922075704/http://folding.typepad.com/news/2008/04/gpu2-open-bet-1.html |archive-date=September 22, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU2 goes live">{{cite web|url=http://folding.typepad.com/news/2008/04/updates-to-the.html |title=Updates to the Download page/GPU2 goes live |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 15, 2008 |access-date=September 7, 2011 |archive-url=https://web.archive.org/web/20121018235447/http://folding.typepad.com/news/2008/04/updates-to-the.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: Simbios">{{cite web|url=http://folding.typepad.com/news/2008/04/foldinghome-and.html |title=Folding@home and Simbios |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 23, 2008 |access-date=November 9, 2011 |archive-url=https://web.archive.org/web/20121018225619/http://folding.typepad.com/news/2008/04/foldinghome-and.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU news">{{cite web|url=http://folding.typepad.com/news/2008/05/gpu-news-gpu1-g.html |title=GPU news (about GPU1, GPU2, & NVIDIA support) |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=May 23, 2008 |access-date=September 8, 2011 |archive-url=https://web.archive.org/web/20121018230744/http://folding.typepad.com/news/2008/05/gpu-news-gpu1-g.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: what does SMP do">{{cite web|url=http://folding.typepad.com/news/2008/06/what-does-the-smp-core-do.html |title=What does the SMP core do? |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=June 15, 2008 |access-date=September 7, 2011 |archive-url=https://web.archive.org/web/20121003174852/http://folding.typepad.com/news/2008/06/what-does-the-smp-core-do.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: life with PS">{{cite web|url=http://folding.typepad.com/news/2008/09/life-with-playstation.html |title=Life with Playstation&nbsp;– a new update to the FAH/PS3 client |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=September 18, 2008 |access-date=February 24, 2012 |archive-url=https://web.archive.org/web/20121018231656/http://folding.typepad.com/news/2008/09/life-with-playstation.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: possible alz. drug">{{cite web|url=http://folding.typepad.com/news/2008/12/new-fah-results-on-possible-new-alzheimers-drug-presented.html |title=New FAH results on possible new Alzheimer's drug presented |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=December 18, 2008 |access-date=September 23, 2011 |archive-url=https://web.archive.org/web/20120908032829/http://folding.typepad.com/news/2008/12/new-fah-results-on-possible-new-alzheimers-drug-presented.html |archive-date=September 8, 2012 |url-status=live  }}</ref>

<ref name="typepad: FAH passes 5 PF">{{cite web|url=http://folding.typepad.com/news/2009/02/foldinghome-passes-the-5-petaflop-mark.html |title=Folding@home Passes the 5 petaFLOP Mark |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=February 18, 2009 |access-date=August 31, 2011 |archive-url=https://web.archive.org/web/20120908171957/http://folding.typepad.com/news/2009/02/foldinghome-passes-the-5-petaflop-mark.html |archive-date=September 8, 2012 |url-status=live  }}</ref>

<ref name="typepad: how does dev get done">{{cite web|url=http://folding.typepad.com/news/2009/06/how-does-fah-code-development-and-sysadmin-get-done.html |title=How does FAH code development and sysadmin get done? |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=June 17, 2009 |access-date=October 14, 2011 |archive-url=https://web.archive.org/web/20121003174914/http://folding.typepad.com/news/2009/06/how-does-fah-code-development-and-sysadmin-get-done.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: update on new FahCores">{{cite web|url=http://folding.typepad.com/news/2009/09/update-on-new-fah-cores-and-clients.html |title=Update on new FAH cores and clients |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=September 25, 2009 |access-date=February 24, 2012 |archive-url=https://web.archive.org/web/20121003175132/http://folding.typepad.com/news/2009/09/update-on-new-fah-cores-and-clients.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: protomol b4">{{cite web|url=http://folding.typepad.com/news/2009/12/release-of-new-protomol-core-b4-wus-.html |title=Release of new Protomol (Core B4) WUs |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=December 22, 2009 |access-date=September 23, 2011 |archive-url=https://web.archive.org/web/20121003175047/http://folding.typepad.com/news/2009/12/release-of-new-protomol-core-b4-wus-.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU3 prep">{{cite web|url=http://folding.typepad.com/news/2010/04/prepping-for-the-gpu3-rolling-new-client-and-nvidia-fah-gpu-clients-will-need-cuda-22-or-later.html |title=Prepping for the GPU3 rolling: new client and NVIDIA FAH GPU clients will (in the future) need CUDA 2.2 or later |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 24, 2010 |access-date=September 8, 2011 |archive-url=https://web.archive.org/web/20121018220820/http://folding.typepad.com/news/2010/04/prepping-for-the-gpu3-rolling-new-client-and-nvidia-fah-gpu-clients-will-need-cuda-22-or-later.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: GPU3 open beta">{{cite web|url=http://folding.typepad.com/news/2010/05/open-beta-release-of-the-gpu3-clientcore.html |title=Folding@home: Open beta release of the GPU3 client/core |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=May 25, 2010 |access-date=September 7, 2011 |archive-url=https://web.archive.org/web/20121003173740/http://folding.typepad.com/news/2010/05/open-beta-release-of-the-gpu3-clientcore.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: ATI core 16 released">{{cite web|url=http://folding.typepad.com/news/2011/03/core-16-for-ati-released-also-note-on-nvidia-gpu-support-for-older-boards.html |title=Core 16 for ATI released; also note on NVIDIA GPU support for older boards |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=March 31, 2011 |access-date=September 7, 2011 |archive-url=https://web.archive.org/web/20121003173735/http://folding.typepad.com/news/2011/03/core-16-for-ati-released-also-note-on-nvidia-gpu-support-for-older-boards.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: V7 in open beta">{{cite web|url=http://folding.typepad.com/news/2011/03/client-version-7-now-in-open-beta.html |title=Client version 7 now in open beta |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=March 29, 2011 |access-date=August 14, 2011 |archive-url=https://web.archive.org/web/20121003173731/http://folding.typepad.com/news/2011/03/client-version-7-now-in-open-beta.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: more transparency">{{cite web|url=http://folding.typepad.com/news/2011/04/more-transparency-in-testing.html |title=More transparency in testing |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=April 5, 2011 |access-date=October 14, 2011 |archive-url=https://web.archive.org/web/20121018230412/http://folding.typepad.com/news/2011/04/more-transparency-in-testing.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: bigadv points change">{{cite web|url=http://folding.typepad.com/news/2011/07/change-in-the-points-system-for-bigadv-work-units.html |title=Change in the points system for bigadv work units |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=July 2, 2011 |access-date=February 24, 2012 |archive-url=https://web.archive.org/web/20121018220238/http://folding.typepad.com/news/2011/07/change-in-the-points-system-for-bigadv-work-units.html |archive-date=October 18, 2012 |url-status=live  }}</ref>

<ref name="typepad: comparison with Anton">{{cite web|url=http://folding.typepad.com/news/2011/10/comparison-between-fah-and-antons-approaches.html |title=Comparison between FAH and Anton's approaches |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=October 13, 2011 |access-date=February 25, 2012 |archive-url=https://web.archive.org/web/20121005084938/http://folding.typepad.com/news/2011/10/comparison-between-fah-and-antons-approaches.html |archive-date=October 5, 2012 |url-status=live  }}</ref>

<ref name="typepad: update on bigadv-16">{{cite web|url=http://folding.typepad.com/news/2012/02/update-on-bigadv-16-the-new-bigadv-rollout.html |title=Update on "bigadv-16", the new bigadv rollout |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=February 7, 2012 |access-date=February 9, 2012 |archive-url=https://web.archive.org/web/20121003175419/http://folding.typepad.com/news/2012/02/update-on-bigadv-16-the-new-bigadv-rollout.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: kasson update">{{cite web|url=http://folding.typepad.com/news/2012/02/update-from-the-kasson-lab-at-the-university-of-virginia.html |title=Protein folding and viral infection |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=February 24, 2012 |access-date=March 4, 2012 |archive-url=https://web.archive.org/web/20121003175415/http://folding.typepad.com/news/2012/02/update-from-the-kasson-lab-at-the-university-of-virginia.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: drug design methods">{{cite web|url=http://folding.typepad.com/news/2012/02/new-methods-for-computational-drug-design.html |title=New methods for computational drug design |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=February 27, 2012 |access-date=April 1, 2012 |archive-url=https://web.archive.org/web/20120923042053/http://folding.typepad.com/news/2012/02/new-methods-for-computational-drug-design.html |archive-date=September 23, 2012 |url-status=live  }}</ref>

<ref name="typepad: v7 rollout">{{cite web|url=http://folding.typepad.com/news/2012/03/web-page-revamp-and-v7-rollout.html |title=Web page revamp and v7 rollout |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=March 22, 2012 |access-date=March 22, 2012 |archive-url=https://web.archive.org/web/20121003174839/http://folding.typepad.com/news/2012/03/web-page-revamp-and-v7-rollout.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: how far FAH has come">{{cite web|url=http://folding.typepad.com/news/2012/06/fahcon-2012-thinking-about-how-far-fah-has-come.html |title=FAHcon 2012: Thinking about how far FAH has come |author=Vijay Pande |work=Folding@home |publisher=[[typepad.com]] |date=June 8, 2012 |access-date=June 12, 2012 |archive-url=https://web.archive.org/web/20121003174200/http://folding.typepad.com/news/2012/06/fahcon-2012-thinking-about-how-far-fah-has-come.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="typepad: drug targets">{{cite web|url=http://folding.typepad.com/news/2012/07/searching-for-new-drug-targets.html |title=Searching for new drug targets |author=Gregory Bowman |work=Folding@home |publisher=[[typepad.com]] |date=July 23, 2012 |access-date=September 27, 2011 |archive-url=https://web.archive.org/web/20120921221246/http://folding.typepad.com/news/2012/07/searching-for-new-drug-targets.html |archive-date=September 21, 2012 |url-status=live  }}</ref>

<!-- *** Foldingforum.org posts *** -->

<ref name="papers for free">{{cite web|url=https://foldingforum.org/viewtopic.php?f=16&t=19643&p=197898#p197898 |title=Re: Suggested Changes to F@h Website |author=Vijay Pande |work=Folding@home |publisher=[[phpBB]] Group |date=October 25, 2011 |access-date=October 25, 2011 |archive-url=https://web.archive.org/web/20120331004334/http://foldingforum.org/viewtopic.php?f=16&t=19643&p=197898 |archive-date=March 31, 2012 |url-status=live }}</ref>

<ref name="6 petaFLOPS">{{cite web|url=https://foldingforum.org/viewtopic.php?f=16&t=20011#p198840 |title=Six Native PetaFLOPS |author=Jesse Victors |work=Folding@home |publisher=[[phpBB]] Group |date=November 10, 2011 |access-date=November 11, 2011 |archive-url=https://web.archive.org/web/20130731182615/http://foldingforum.org/viewtopic.php?f=16&t=20011 |archive-date=July 31, 2013 |url-status=live }}</ref>

<ref name="bigadv">{{cite web|url=https://foldingforum.org/viewtopic.php?t=10697 |title=new release: extra-large work units |author=Peter Kasson (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=July 15, 2009 |access-date=October 9, 2011 |archive-url=https://web.archive.org/web/20121111021306/http://foldingforum.org/viewtopic.php?t=10697 |archive-date=November 11, 2012 |url-status=live  }}</ref>

<ref name="SMP2 release">{{cite web|url=https://foldingforum.org/viewtopic.php?f=24&t=13038#p127406 |title=upcoming release of SMP2 cores |author=Peter Kasson (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=January 24, 2010 |access-date=September 30, 2011 |archive-url=https://web.archive.org/web/20121130044906/http://foldingforum.org/viewtopic.php?f=24&t=13038 |archive-date=November 30, 2012 |url-status=live }}</ref>

<ref name="forum: 7.1.38 released">{{cite web|url=https://foldingforum.org/viewtopic.php?f=67&t=19795&start=45#p197198 |title=Re: FAHClient V7.1.38 released (4th Open-Beta) |author=Joseph Coffland (CEO of Cauldron Development LLC & lead developer at Folding@home) |work=Folding@home |publisher=[[phpBB]] Group |date=October 13, 2011 |access-date=October 15, 2011 |archive-url=https://web.archive.org/web/20120331004019/http://foldingforum.org/viewtopic.php?f=67&t=19795&start=45 |archive-date=March 31, 2012 |url-status=live }}</ref>

<ref name="forum: 7610/7611 in beta">{{cite web|url=https://foldingforum.org/viewtopic.php?f=66&t=18822 |title=Project 7610 & 7611 in Beta |author=TJ Lane (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=June 6, 2011 |access-date=February 25, 2012 |archive-url=https://web.archive.org/web/20140809222806/https://foldingforum.org/viewtopic.php?f=66&t=18822 |archive-date=August 9, 2014 |url-status=live }}{{registration required}}</ref>

<ref name="forum: GPU3 headless guide">{{cite web|url=https://foldingforum.org/viewtopic.php?f=54&t=6793 |title=NVIDIA GPU3 Linux/Wine Headless Install Guide |work=Folding@home |publisher=[[phpBB]] Group |date=November 8, 2008 |access-date=September 5, 2011 |archive-url=https://web.archive.org/web/20121009061606/http://foldingforum.org/viewtopic.php?f=54&t=6793 |archive-date=October 9, 2012 |url-status=live }}</ref>

<ref name="forum: FAH EULA">{{cite web|url=https://foldingforum.org/viewtopic.php?f=24&t=3600 |title=Folding@home's End User License Agreement (EULA) |author=Vijay Pande |work=Folding@home |date=June 28, 2008 |access-date=May 15, 2012 |archive-url=https://web.archive.org/web/20121009070038/http://foldingforum.org/viewtopic.php?f=24&t=3600 |archive-date=October 9, 2012 |url-status=live }}</ref>

<ref name="forum: can FAH damage PC?">{{cite web|url=https://foldingforum.org/viewtopic.php?f=50&t=15863#p157125 |title=Re: Can Folding@home damage any part of my PC? |author=PantherX |work=Folding@home |publisher=[[phpBB]] Group |date=September 2, 2010 |access-date=February 25, 2012 |archive-url=https://web.archive.org/web/20121130111533/http://foldingforum.org/viewtopic.php?f=50&t=15863 |archive-date=November 30, 2012 |url-status=live }}</ref>

<ref name="forum: troubleshooting bad WUs">{{cite web|url=https://foldingforum.org/viewtopic.php?f=19&t=16526 |title=Troubleshooting Bad WUs |author=PantherX |work=Folding@home |publisher=[[phpBB]] Group |date=October 31, 2010 |access-date=August 7, 2011 |archive-url=https://web.archive.org/web/20121007034441/http://foldingforum.org/viewtopic.php?f=19&t=16526 |archive-date=October 7, 2012 |url-status=live }}</ref>

<ref name="forum: 6803(4,66,255)">{{cite web|url=https://foldingforum.org/viewtopic.php?f=19&t=19725#p196444 |title=Re: Project 6803: (Run 4, Clone 66, Gen 255) |author=PantherX |work=Folding@home |publisher=[[phpBB]] Group |date=October 1, 2011 |access-date=October 9, 2011 |archive-url=https://web.archive.org/web/20120331003831/http://foldingforum.org/viewtopic.php?f=19&t=19725 |archive-date=March 31, 2012 |url-status=live }}</ref>

<ref name="forum: 10125">{{cite web |url= https://foldingforum.org/viewtopic.php?f=66&t=19423&p=193871#p193871 |title= Project 10125 |author= Gregory Bowman (Pande lab Member) |work= Folding@home |publisher= [[phpBB]] Group |access-date= December 2, 2011}}{{registration required |archive-url= https://www.webcitation.org/6Aqt4nOWS?url=http://foldingforum.org/viewtopic.php?f%3D66%26t%3D19423%26p%3D193871 |archive-date= September 20, 2012 |url-status= live}}</ref>

<ref name="forum: 7600 in beta">{{cite web|url=https://foldingforum.org/viewtopic.php?f=66&t=18839 |title=Project 7600 in Beta |author=TJ Lane (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=June 8, 2011 |access-date=September 27, 2011 |archive-url=https://web.archive.org/web/20140810001102/https://foldingforum.org/viewtopic.php?f=66&t=18839 |archive-date=August 10, 2014 |url-status=live }}{{registration required}}</ref>

<ref name="forum: 8021 in beta">{{cite web|url=https://foldingforum.org/viewtopic.php?f=66&t=20765&p=207880 |title=Project 8021 released to beta |author=Diwakar Shukla (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=February 10, 2012 |access-date=March 17, 2012 |archive-url=https://web.archive.org/web/20140809223548/https://foldingforum.org/viewtopic.php?f=66&t=20765&p=207880 |archive-date=August 9, 2014 |url-status=live }}{{registration required}}</ref>

<ref name="forum: 6871">{{cite web|url=https://foldingforum.org/viewtopic.php?f=66&t=19201&p=191821 |title=New project p6871 [Classic] |author=yslin (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=July 22, 2011 |access-date=March 17, 2012 |archive-url=https://web.archive.org/web/20131030165821/https://foldingforum.org/viewtopic.php?f=66&t=19201&p=191821 |archive-date=October 30, 2013 |url-status=live }}{{registration required}}</ref>

<ref name="forum: 7808/7809 to FAH">{{cite web|url=https://foldingforum.org/viewtopic.php?f=24&t=19376&start=0#p193378 |title=Projects 7808 and 7809 to full fah |author=Christian "schwancr" Schwantes (Pande lab member) |work=Folding@home |publisher=[[phpBB]] Group |date=August 15, 2011 |access-date=October 16, 2011 |archive-url=https://web.archive.org/web/20130131223022/http://foldingforum.org/viewtopic.php?f=24&t=19376&start=0 |archive-date=January 31, 2013 |url-status=live }}</ref>

<ref name="forum: Gromacs cannot continue">{{cite web|url=https://foldingforum.org/viewtopic.php?f=59&t=19315#p192836 |title=Re: Gromacs Cannot Continue Further |author=Bruce Borden |work=Folding@home |publisher=[[phpBB]] Group |date=August 7, 2011 |access-date=August 7, 2011 |archive-url=https://web.archive.org/web/20120331002821/http://foldingforum.org/viewtopic.php?f=59&t=19315 |archive-date=March 31, 2012 |url-status=live }}</ref>

<ref name="forum: core17 Linux">{{cite web |url= https://foldingforum.org/viewtopic.php?f=88&t=24469 |title= GPU FahCore_17 is now available on Windows & native Linux |author= Bruce Borden |work= Folding@home |publisher= [[phpBB]] Group |date= June 25, 2013 |access-date= September 30, 2014}}</ref>

<!-- *** Miscellaneous websites *** -->

<ref name="Copernicus download">{{cite web|url=http://copernicus-computing.org/?q=node/2 |title=Copernicus Download |author1=Sander Pronk |author2=Iman Pouya |author3=Per Larsson |author4=Peter Kasson |author5=Erik Lindahl |work=copernicus-computing.org |publisher=Copernicus |date=November 17, 2011 |access-date=October 2, 2012 |archive-url=https://web.archive.org/web/20121007045701/http://copernicus-computing.org/?q=node/2 |archive-date=October 7, 2012 |url-status=live  }}</ref>

<ref name="MSMBuilder source">{{cite web|url=https://simtk.org/scm/instructions.php/msmbuilder |title=MSMBuilder Source Code Repository |work=MSMBuilder |publisher=simtk.org |year=2012 |access-date=October 12, 2012 |archive-url=https://archive.today/20121228125516/https://simtk.org/scm/instructions.php/msmbuilder |archive-date=December 28, 2012 |url-status=live  }}</ref>

<ref name="past 4 petaFLOPS">{{cite web|url=http://team52735.blogspot.com/2008_09_29_archive.html |title=Increase in 'active' PS3 folders pushes Folding@home past 4 Petaflops! |work=team52735.blogspot.com |publisher=[[Blogspot]] |date=September 29, 2008 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20131222204303/http://team52735.blogspot.com/2008_09_29_archive.html |archive-date=December 22, 2013 |url-status=live  }}</ref>

<ref name="Biotech 27">{{cite web|url=http://castroller.com/Podcasts/FuturesInBiotech/249153 |title=Futures in Biotech 27: Folding@home at 1.3 Petaflops |format=Interview, webcast |work=Castroller.com |publisher=CastRoller |date=December 28, 2007 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20111129214623/http://castroller.com/Podcasts/FuturesInBiotech/249153 |archive-date=November 29, 2011 |url-status=dead  }}</ref>

<ref name="cnn ps3">{{cite web|url=http://edition.cnn.com/2006/TECH/fun.games/09/18/playstation.folding/ |title=PlayStation's serious side: Fighting disease |author=David E. Williams |publisher=CNN |date=October 20, 2006 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120622021742/http://edition.cnn.com/2006/TECH/fun.games/09/18/playstation.folding/ |archive-date=June 22, 2012 |url-status=live  }}</ref>

<ref name="2010 KPS award">{{cite web|url=https://simtk.org/project/xml/news.xml?group_id=357 |title=Greg Bowman awarded the 2010 Kuhn Paradigm Shift Award |work=simtk.org |publisher=SimTK: MSMBuilder |date=March 29, 2010 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120407122326/https://simtk.org/project/xml/news.xml?group_id=357 |archive-date=April 7, 2012 |url-status=live  }}</ref>

<ref name="Biophysical society names recipients">{{cite web |url=http://www.biophysics.org/LinkClick.aspx?fileticket=k_JYSLGevzU%3d&tabid=504 |title=Biophysical Society Names Five 2012 Award Recipients |work=Biophysics.org |publisher=Biophysical Society |date=August 17, 2011 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120327180426/http://www.biophysics.org/LinkClick.aspx?fileticket=k_JYSLGevzU%3D&tabid=504 |archive-date=March 27, 2012 |url-status=dead }}</ref>

<ref name="FAH publishes cancer results">{{cite news|url=http://www.maximumpc.com/forums/viewtopic.php?p=112590 |title=F@H project publishes results of cancer related research |author=((mah3)) |author2=Vijay Pande |work=[[MaximumPC]].com |publisher=Future US, Inc. |date=September 24, 2004 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20131029210338/http://www.maximumpc.com/forums/viewtopic.php?p=112590 |archive-date=October 29, 2013 |url-status=live  }} ''To our knowledge, this is the first peer-reviewed results from a distributed computing project related to cancer.''</ref>

<ref name="Peter Kasson">{{cite web |url=http://bme.virginia.edu/people/kasson.html |title=Peter M. Kasson |author=Peter Kasson |work=Kasson lab |publisher=[[University of Virginia]] |year=2012 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120903200810/http://bme.virginia.edu/people/kasson.html |archive-date=September 3, 2012 |url-status=dead  }}</ref>

<ref name="scientists boost IL-2 potency">{{cite web|url=http://medicalxpress.com/news/2012-03-scientists-boost-potency-side-effects.html |title=Scientists boost potency, reduce side effects of IL-2 protein used to treat cancer |work=MedicalXpress.com |publisher=Medical Xpress |date=March 18, 2012 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20121003154151/http://medicalxpress.com/news/2012-03-scientists-boost-potency-side-effects.html |archive-date=October 3, 2012 |url-status=live  }}</ref>

<ref name="Top500 June 2007">{{cite web |url= http://www.top500.org/list/2007/06/100 |title= TOP500 List&nbsp;— June 2007 |work= top500.org |publisher= [[Top500]] |date= June 2007 |access-date= September 20, 2012 |archive-date= September 30, 2007 |archive-url= https://web.archive.org/web/20070930201044/http://www.top500.org/list/2007/06/100 |url-status= dead }}</ref>

<ref name="Top500 November 2008">{{cite web |url= http://www.top500.org/list/2008/11/100 |title= TOP500 List&nbsp;— November 2008 |work= top500.org |publisher= [[Top500]] |date= November 2008 |access-date= September 20, 2012 |archive-date= December 9, 2008 |archive-url= https://web.archive.org/web/20081209070813/http://www.top500.org/list/2008/11/100 |url-status= dead }}</ref>

<ref name="FAH reaches 2 PF">{{cite web|url=http://n4g.com/news/143113/ps3-andamp-foldingahome-reach-2-petaflops |title=Folding@Home reach 2 Petaflops |work=n4g.com |publisher=HAVAmedia |date=May 8, 2008 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120610010619/http://n4g.com/news/143113/ps3-andamp-foldingahome-reach-2-petaflops |archive-date=June 10, 2012 |url-status=live  }}</ref>

<ref name="Nvidia-FAH milestone">{{cite web |url= http://www.nvidia.com/object/io_1219747545128.html |title= NVIDIA Achieves Monumental Folding@Home Milestone With Cuda |work= nvidia.com |publisher= [[NVIDIA Corporation]] |date= August 26, 2008 |access-date= September 20, 2012}}</ref>

<ref name="3 PF barrier">{{cite web|url=http://www.longecity.org/forum/topic/23841-3-petaflop-barrier/ |title=3 PetaFLOP barrier |work=longecity.org |publisher=Longecity |date=August 19, 2008 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120830095443/http://www.longecity.org/forum/topic/23841-3-petaflop-barrier/ |archive-date=August 30, 2012 |url-status=live  }}</ref>

<ref name="Community Grid Computing">{{cite web |url=http://cs-alb-pc3.massey.ac.nz/notes/59735/seminars/06235808.pdf |title=Community Grid Computing&nbsp;— Studies in Parallel and Distributed Systems |author=Dragan Zakic |work=Massey University College of Sciences |publisher=[[Massey University]] |date=May 2009 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120323214701/http://cs-alb-pc3.massey.ac.nz/notes/59735/seminars/06235808.pdf |archive-date=March 23, 2012 |url-status=dead  }}</ref>

<ref name="crossing 5 PF barrier">{{cite web|url=http://www.longecity.org/forum/topic/26449-crossing-the-5-petaflops-barrier/ |title=Crossing the 5 petaFLOPS barrier |work=longecity.org |publisher=Longecity |date=February 18, 2009 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120830095559/http://www.longecity.org/forum/topic/26449-crossing-the-5-petaflops-barrier/ |archive-date=August 30, 2012 |url-status=live  }}</ref>

<ref name="review of FAH">{{cite web |url=http://biochem218.stanford.edu/Projects%202010/Ito%202010.pdf |title=A review of recent advances in ab initio protein folding by the Folding@home project |author=William Ito |publisher=foldingathome.org |access-date=September 22, 2012 |archive-url=https://web.archive.org/web/20110331165902/http://biochem218.stanford.edu/Projects%202010/Ito%202010.pdf |archive-date=March 31, 2011 |url-status=dead  }}</ref>

<ref name="Extreme overclocking forum">{{cite web|url=http://forums.extremeoverclocking.com/forumdisplay.php?f=45 |title=Official Extreme Overclocking Folding@home Team Forum |work=forums.extremeoverclocking.com |publisher=Extreme Overclocking |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120921141240/http://forums.extremeoverclocking.com/forumdisplay.php?f=45 |archive-date=September 21, 2012 |url-status=live  }}</ref>

<ref name="MaximumPC Chimp Challenge">{{cite news|url=http://www.maximumpc.com/article/news/help_maximum_pcs_folding_team_win_next_chimp_challenge |title=Help Maximum PC's Folding Team Win the Next Chimp Challenge! |author=Norman Chan |work=Maximumpc.com |publisher=Future US, Inc. |date=April 6, 2009 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120707061249/http://www.maximumpc.com/article/news/help_maximum_pcs_folding_team_win_next_chimp_challenge |archive-date=July 7, 2012 |url-status=live  }}</ref>

<ref name="help ubuntu">{{cite web|url=https://help.ubuntu.com/community/FoldingAtHome |title=FoldingAtHome |author=unikuser |work=Ubuntu Documentation |publisher=help.ubuntu.com |date=August 7, 2011 |access-date=September 22, 2012 |archive-url=https://web.archive.org/web/20120422031744/https://help.ubuntu.com/community/FoldingAtHome |archive-date=April 22, 2012 |url-status=live  }}</ref>

<ref name="FAH for BOINC soon">{{cite web|url=http://www.boarddigger.com/forum/gxbovGYpO1F |title=Folding@home client for BOINC in beta "soon" |author=Rattledagger, Vijay Pande |work=Boarddigger.com |publisher=Anandtech.com |date=April 1, 2005 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120917144907/http://www.boarddigger.com/forum/gxbovGYpO1F |archive-date=September 17, 2012 |url-status=live  }}</ref>

<ref name="PS3 to study cancer">{{cite web |url=http://www.mb.com.ph/node/11811 |title=The Home Cure: PlayStation 3 to Help Study Causes of Cancer |author=Jerry Liao |work=mb.com |publisher=Manila Bulletin Publishing Corporation |date=March 23, 2007 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120701221323/http://www.mb.com.ph/node/11811 |archive-date=July 1, 2012 |url-status=dead  }}</ref>

<ref name="PS3 research project">{{cite news|url=http://old.post-gazette.com/pg/07085/772011-96.stm |title=Week in video-game news: 'God of War II' storms the PS2; a PS3 research project |author=Lou Kesten, [[Associated Press]] |work=Post-Gazette.com |publisher=[[Pittsburgh Post-Gazette]] |date=March 26, 2007 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120620152335/http://old.post-gazette.com/pg/07085/772011-96.stm |archive-date=June 20, 2012 |url-status=live  }}</ref>

<ref name="Life With PS3 live">{{cite web|url=https://gizmodo.com/5051558/ps3-news-service-life-with-playstation-now-up-for-download |title=PS3 News Service, Life With Playstation, Now Up For Download |author=Elaine Chow |work=Gizmodo.com |publisher=[[Gizmodo]] |date=September 18, 2008 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20120620105641/http://gizmodo.com/5051558/ps3-news-service-life-with-playstation-now-up-for-download |archive-date=June 20, 2012 |url-status=live  }}</ref>

<ref name="PS3 4.30 update, drop F@h">{{cite web|url=http://blog.us.playstation.com/2012/10/21/ps3-system-software-update-v4-30/ |title=PS3 System Software Update (v4.30) |author=Eric Lempel |work=PlayStation blog |publisher=[[Sony]] |date=October 21, 2012 |access-date=October 21, 2012 |archive-url=https://web.archive.org/web/20121024031711/http://blog.us.playstation.com/2012/10/21/ps3-system-software-update-v4-30/ |archive-date=October 24, 2012 |url-status=live  }}</ref>

<ref name="LWP termination">{{cite web|url=http://www.playstation.com/life/en/index.html |title=Termination of Life with PlayStation |work=Life with PlayStation |publisher=[[Sony]] |date=November 6, 2012 |access-date=November 8, 2012 |archive-url=https://web.archive.org/web/20121113072624/http://www.playstation.com/life/en/index.html |archive-date=November 13, 2012 |url-status=dead  }}</ref>

<ref name="Ticket #736">{{cite web |url=https://fah-web.stanford.edu/projects/FAHClient/ticket/736 |title=Ticket #736 (Link to GPL in FAHControl) |author1=aschofield |author2=jcoffland |work=Folding@home |publisher=[[Trac]] |date=October 3, 2011 |access-date=October 12, 2012 |archive-url=https://web.archive.org/web/20120528065636/https://fah-web.stanford.edu/projects/FAHClient/ticket/736 |archive-date=May 28, 2012 |url-status=dead  }}</ref>

<ref name="FAHControl source code">{{cite web |url= https://fah-web.stanford.edu/svn/pub/trunk/control/ |archive-url= https://archive.today/20121212232230/https://fah-web.stanford.edu/svn/pub/trunk/control/ |url-status= dead |archive-date= December 12, 2012 |title=FAHControl source code repository |author=Folding@home developers |publisher=foldingathome.org |access-date=October 15, 2012}}</ref>

<ref name="F@H vs R@h">{{cite web|url=http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1790 |title=Folding@home vs. Rosetta@home |author=Gen_X_Accord, Vijay Pande |work=[[Rosetta@home]] forums |publisher=[[University of Washington]] |date=June 11, 2006 |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20140808143458/http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1790 |archive-date=August 8, 2014 |url-status=live  }}</ref>

<ref name="FAH stats doc">{{cite web |url= https://docs.google.com/spreadsheet/ccc?key=0AtDZlHnA_WpldGFiM184dnpJbllrck50NnJnUS1CdVE#gid=0 |title= Folding@home Stats - Google Docs |author= Risto Kantonen |work= Folding@home |date= September 23, 2013 |access-date= September 23, 2013 }}</ref>

<ref name="FAH leadership change">{{cite web |url= https://source.wustl.edu/2019/02/computational-biology-project-aims-to-better-understand-protein-folding/ |title= Computational biology project aims to better understand protein folding |author= Julia Evangelou Strait |date= February 26, 2019 |access-date= March 8, 2020 }}</ref>

}}

== Sources ==
* {{Citation |author1=Folding@home |title=About |url=https://foldingathome.org/about/ |website=Folding@home |access-date=April 26, 2020 |date=n.d.e}}
* {{Citation |last1=Mims |first1=Christopher |title=Why China's New Supercomputer Is Only Technically the World's Fastest |date=November 8, 2010 |url=http://www.technologyreview.com/view/421584/why-chinas-new-supercomputer-is-only-technically/ |website=Technology Review |publisher=MIT |access-date=September 20, 2012 |archive-url=https://web.archive.org/web/20121021194240/http://www.technologyreview.com/view/421584/why-chinas-new-supercomputer-is-only-technically/ |url-status=dead |archive-date=October 21, 2012}}
* {{Citation |author1=((News 12 Staff)) |title=Hofstra University lends resource lab for worldwide COVID-19 research |url=http://longisland.news12.com/story/42124863/hofstra-university-lends-resource-lab-for-worldwide-covid19-research |access-date=May 24, 2020 |date=May 13, 2020}}
* {{Citation |last1=Pande |first1=Vijay S. |title=Re: ATI and NVIDIA stats vs. PPD numbers |date=November 10, 2008 |url=http://foldingforum.org/viewtopic.php?p=67416 |website=Folding Forum |access-date=April 26, 2020 |archive-url=https://web.archive.org/web/20120331003437/http://foldingforum.org/viewtopic.php?p=67416 |archive-date=March 31, 2012 |url-status=dead |at=the fifth post from below}}

== External links ==
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{{Spoken Wikipedia|En-Folding@home-article.ogg|date=2014-10-07}}

{{Health software}}
{{PlayStation 3}}

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