Editing Structural bioinformatics (section)

=== 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
|}