Editing Structural bioinformatics (section)

== Protein Data Bank (PDB) ==
{{main|Protein Data Bank}}
[[File:Number of structures of Protein Data Bank (1976-2020).png|thumb|The number of structures from PDB. (A) The overall growth of released structures in Protein DataBank per year. (B) Growth of structures deposited in PDB from [[X-ray crystallography]], [[NMR spectroscopy]], and 3D electron microscopy experiments per year. Source: <nowiki>https://www.rcsb.org/stats/growth</nowiki>|alt=|335x335px]]

The [[Protein Data Bank|Protein Data Bank (PDB)]] is a database of 3D structure data for large biological molecules, such as [[protein]]s, [[DNA]], and [[RNA]]. PDB is managed by an international organization called the Worldwide Protein Data Bank ([[Worldwide Protein Data Bank|wwPDB]]), which is composed of several local organizations, as. PDBe, PDBj, RCSB, and BMRB. They are responsible for keeping copies of PDB data available on the internet at no charge. The number of structure data available at PDB has increased each year, being obtained typically by [[X-ray crystallography]], [[Nuclear magnetic resonance spectroscopy|NMR spectroscopy]], or [[Cryogenic electron microscopy|cryo-electron microscopy]].

=== Data format ===
The [[Protein Data Bank (file format)|PDB format]] (.pdb) is the legacy textual file format used to store information of three-dimensional structures of macromolecules used by the Protein Data Bank. Due to restrictions in the format structure conception, the PDB format does not allow large structures containing more than 62 chains or 99999 atom records.<ref>{{Cite web|url=http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html|title=PDBx/mmCIF General FAQ|website=mmcif.wwpdb.org|access-date=2020-02-26}}</ref>

The PDBx/[[mmCIF]] (macromolecular Crystallographic Information File) is a standard text file format for representing crystallographic information.<ref>{{Cite web|url=https://www.wwpdb.org/documentation/file-formats-and-the-pdb|title=wwPDB: File Formats and the PDB|last=wwPDB.org|website=www.wwpdb.org|language=en|access-date=2020-02-26}}</ref> Since 2014, the PDB format was substituted as the standard PDB archive distribution by the PDBx/mmCIF file format (.cif). While PDB format contains a set of records identified by a keyword of up to six characters, the PDBx/mmCIF format uses a structure based on key and value, where the key is a name that identifies some feature and the value is the variable information.<ref>{{Cite web|url=http://mmcif.wwpdb.org/docs/pubs/methods-enzymology-paper-1997.html|title=PDBx/mmCIF Dictionary Resources|website=mmcif.wwpdb.org|access-date=2020-02-26}}</ref>

=== Other structural databases ===
In addition to the [[Protein Data Bank|Protein Data Bank (PDB)]], there are several databases of protein structures and other macromolecules. Examples include:

* '''[[MMDB]]''': Experimentally determined three-dimensional structures of biomolecules derived from Protein Data Bank (PDB).<ref>{{Cite web|url=https://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml|title=Macromolecular Structures Resource Group|website=www.ncbi.nlm.nih.gov|access-date=2020-04-13}}</ref>
* '''Nucleic acid Data Base (NDB):''' Experimentally determined information about nucleic acids (DNA, RNA).<ref>{{Cite web|url=http://ndbserver.rutgers.edu/|title=Nucleic Acid Database (NDB)|website=ndbserver.rutgers.edu|access-date=2020-04-13}}</ref>
* '''[[Structural Classification of Proteins database|Structural Classification of Proteins (SCOP)]]:''' Comprehensive description of the structural and evolutionary relationships between structurally known proteins.<ref>{{Cite web|url=http://scop.mrc-lmb.cam.ac.uk/scop/|title=SCOP: Structural Classification of Proteins|date=2007-09-11|archive-url=https://web.archive.org/web/20070911012207/http://scop.mrc-lmb.cam.ac.uk/scop/|access-date=2020-04-13|archive-date=2007-09-11}}</ref>
* '''TOPOFIT-DB:''' Protein structural alignments based on the TOPOFIT method.<ref>{{cite journal | vauthors = Ilyin VA, Abyzov A, Leslin CM | title = Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point | journal = Protein Science | volume = 13 | issue = 7 | pages = 1865–74 | date = July 2004 | pmid = 15215530 | pmc = 2279929 | doi = 10.1110/ps.04672604 }}</ref>
* '''Electron Density Server (EDS):''' Electron-density maps and statistics about the fit of crystal structures and their maps.<ref>{{Cite web|url=http://eds.bmc.uu.se/eds/|title=EDS - Uppsala Electron Density Server|website=eds.bmc.uu.se|access-date=2020-04-13}}</ref>
* '''[[CASP]]:''' Prediction Center Community-wide, worldwide experiment for protein structure prediction [[CASP]].<ref>{{Cite web|url=http://www.predictioncenter.org/|title=Home - Prediction Center|website=www.predictioncenter.org|access-date=2020-04-13}}</ref>
* '''PISCES server for creating non-redundant lists of proteins:''' Generates PDB list by sequence identity and structural quality criteria.<ref>{{Cite web|url=http://dunbrack.fccc.edu/PISCES.php|title=:: Dunbrack Lab|website=dunbrack.fccc.edu|access-date=2020-04-13}}</ref>
* '''The Structural Biology Knowledgebase:''' Tools to aid in protein research design.<ref>{{Cite web|url=http://sbkb.org/|title=Structural Biology KnowlegebaseSBKB - SBKB|website=sbkb.org|access-date=2020-04-13}}</ref>
* '''[[ProtCID]]:''' The Protein Common Interface Database Database of similar protein-protein interfaces in crystal structures of homologous proteins.<ref>{{Cite web|url=http://dunbrack2.fccc.edu/protcid|title=Protein Common Interface Database|website=dunbrack2.fccc.edu|access-date=2020-04-13}}</ref>
* '''[[AlphaFold]]:'''AlphaFold - Protein Structure Database.<ref>{{Cite web|url=https://alphafold.ebi.ac.uk|title=AlphaFold}}</ref>