Editing Structural bioinformatics (section)

== Applications ==
[[Informatics]] approaches used in structural bioinformatics are:
* Selection of Target - Potential targets are identified by comparing them with databases of known structures and sequence. The importance of a target can be decided on the basis of published literature. Target can also be selected on the basis of its [[protein domain]]. Protein domains are building blocks that can be rearranged to form new proteins. They can be studied in isolation initially.
* Tracking [[X-ray crystallography]] trials - X-Ray crystallography can be used to reveal three-dimensional structure of a protein. But, in order to use X-ray for studying protein crystals, pure proteins crystals must be formed, which can take a lot of trials. This leads to a need for tracking the conditions and results of trials. Furthermore, supervised machine learning algorithms can be used on the stored data to identify conditions that might increase the yield of pure crystals. 
* Analysis of X-Ray crystallographic data - The diffraction pattern obtained as a result of bombarding X-rays on electrons is [[Fourier transform]] of electron density distribution. There is a need for algorithms that can deconvolve Fourier transform with partial information ( due to missing phase information, as the detectors can only measure amplitude of diffracted X-rays, and not the phase shifts ). Extrapolation technique such as [[Multiwavelength anomalous dispersion]] can be used to generate electron density map, which uses the location of selenium atoms as a reference to determine rest of the structure. Standard [[Ball-and-stick model]] is generated from the electron density map. 
* Analysis of NMR spectroscopy data - [[Nuclear magnetic resonance spectroscopy]] experiments produce two (or higher) dimensional data, with each peak corresponding to a chemical group within the sample. Optimization methods are used to convert spectra into three dimensional structures.
* Correlating Structural information with functional information - Structural studies can be used as probe for structural-functional relationship.

=== Tools ===
{| class="wikitable"
|+List of structural bioinformatics tools
!Software
!Description
|-
|[[I-TASSER]] 
|Predicting three-dimensional structure model of protein molecules from amino acid sequences.
|-
|[[Molecular Operating Environment|MOE]] 
|Molecular Operating Environment (MOE) is an extensive platform including structural modeling for proteins, protein families and antibodies<ref>[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm MOE]</ref> 
|-
|[http://sbl.inria.fr SBL] 
|The Structural Bioinformatics Library: end-user applications and advanced algorithms
|-
|[[BALLView]]
|Molecular modeling and visualization<ref>[http://www.ball-project.org/Ballview BALLView]</ref> 
|-
|[http://www.cbi.cnptia.embrapa.br/SMS STING]
|Visualization and analysis
|-
|[[PyMOL]]
|Viewer and modeling<ref>[http://www.pymol.org/ PyMOL]</ref>
|-
|[[Visual Molecular Dynamics|VMD]] 
|Viewer, molecular dynamics<ref>[http://www.ks.uiuc.edu/Research/vmd/ VMD]</ref>
|-
|[[Gromacs]] 
|Protein folding, molecular dynamics, molecular model refinement, molecular model force field generation<ref>[https://www.gromacs.org/ Gromacs]</ref>
|-
|[[LAMMPS]] 
|Protein folding, molecular dynamics, molecular model refinement, Quantum mechanical macro-molecular interactions<ref>[https://www.lammps.org/#gsc.tab=0 LAMMPS]</ref>
|-
|[[GAMESS]] 
|Molecular Force Field, Charge refinement, Quantum molecular dynamics, Protein-Molecular chemical reaction simulations (electron transfer),<ref>[https://www.msg.chem.iastate.edu/gamess/ GAMESS]</ref>
|-
|[http://kinemage.biochem.duke.edu/software/ KiNG]
|An [[Open-source software|open-source]] Java [[kinemage]] viewer
|-
|[[STRIDE (algorithm)|STRIDE]]
|Determination of secondary structure from coordinates<ref>[https://web.archive.org/web/20010816122006/http://www.embl-heidelberg.de/argos/stride/stride_info.html STRIDE]</ref>
|-
|[[DSSP (algorithm)|DSSP]]
|Algorithm assigning a secondary structure to the amino acids of a protein
|-
|[http://molprobity.biochem.duke.edu/ MolProbity]
|Structure-validation web server
|-
|[https://web.archive.org/web/20080801065546/http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html PROCHECK]
|A structure-validation [[web service]]
|-
|[[CheShift]]
|A protein structure-validation on-line application
|-
|[https://3dmol.csb.pitt.edu/ 3D-mol.js]
|A molecular viewer for web applications developed using Javascript
|-
|[https://web.archive.org/web/20070113065659/http://propka.ki.ku.dk/ PROPKA]
|Rapid prediction of protein pKa values based on empirical structure/function relationships
|-
|[http://cara.nmr.ch/ CARA]
|Computer Aided Resonance Assignment
|-
|[http://www.dockingserver.com/ Docking Server]
|A molecular docking web server
|-
|[http://web.mit.edu/star/biochem StarBiochem]
|A java protein viewer, features direct search of protein databank
|-
|[https://sites.google.com/view/spade SPADE]
|The structural proteomics application development environment
|-
|[http://proline.physics.iisc.ernet.in/pocketsuite/ PocketSuite]
|A web portal for various web-servers for binding site-level analysis. PocketSuite is divided into:: PocketDepth (Binding site prediction)
PocketMatch (Binding site comparison), PocketAlign (Binding site alignment), and PocketAnnotate (Binding site annotation).
|-
|[http://msl-libraries.org MSL]
|An open-source C++ molecular modeling software library for the implementation of structural analysis, prediction and design methods
|-
|[http://zhanglab.ccmb.med.umich.edu/PSSpred/ PSSpred]
|Protein secondary structure prediction
|-
|[http://proteus.dcc.ufmg.br/ Proteus]
|Webtool for suggesting mutation pairs
|-
|[http://marid.bioc.cam.ac.uk/sdm2 SDM]
|A server for predicting effects of mutations on protein stability
|}