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List of protein structure prediction software
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<h2 id="software-list">Software list</h2> <p class="note">Main article: <a href="/facts/Protein_structure_prediction/sj6AbLjI">Protein structure prediction</a></p> <p>Below is a list which separates programs according to the method used for structure prediction. </p> <h3>Homology modeling</h3> <p class="note">Main article: <a href="/facts/Homology_modeling/rgaHkvJX">Homology modeling</a></p> <table><tbody><tr><th>Name</th><th>Method</th><th>Description</th><th>Release date</th></tr><tr><td>IntFOLD</td><td>A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues</td><td>Automated webserver and some downloadable programs</td></tr><tr><td><a href="/facts/RaptorX/dokKrRus">RaptorX</a></td><td>remote homology detection, protein 3D modeling, binding site prediction</td><td>Automated webserver and Downloadable program</td></tr><tr><td><a href="/facts/Biskit/MJUXL4jk">Biskit</a></td><td>wraps external programs into automated workflow</td><td><a href="/facts/BLAST_(biotechnology)/uWufGxFH">BLAST</a> search, <a href="/facts/T-Coffee/kS458MqX">T-Coffee</a> alignment, and <a href="/facts/MODELLER/sb31b8kc">MODELLER</a> construction</td></tr><tr><td><a href="/facts/ESyPred3D/l76x4EdF">ESyPred3D</a></td><td>Template detection, alignment, 3D modeling</td><td>Automated webserver</td></tr><tr><td><a href="/facts/FoldX/vtAzWRtr">FoldX</a></td><td>Energy calculations and protein design</td><td>Downloadable program</td></tr><tr><td><a href="/facts/Phyre/0VX68zFv">Phyre</a>, Phyre2</td><td>Remote template detection, alignment, 3D modeling, multi-templates, <i>ab initio</i></td><td>Webserver with job manager, automatically updated fold library, genome searching and other facilities</td></tr><tr><td><a href="/facts/HH-suite/lIPBDAys">HHpred</a></td><td>Template detection, alignment, 3D modeling</td><td>Interactive webserver with help facility</td></tr><tr><td><a href="/facts/MODELLER/sb31b8kc">MODELLER</a></td><td>Satisfaction of spatial restraints</td><td>Standalone program mainly in <a href="/facts/Fortran/m1KqjcMU">Fortran</a> and <a href="/facts/Python_(programming_language)/YbuGqofa">Python</a></td></tr><tr><td>CONFOLD</td><td>Satisfaction of contact and distance restraints</td><td>Standalone program mainly in <a href="/facts/Fortran/m1KqjcMU">Fortran</a> and <a href="/facts/Perl/fx31kjlT">Perl</a></td></tr><tr><td><a href="/facts/Molecular_Operating_Environment/YmhIJ3dS">Molecular Operating Environment</a> (MOE)</td><td>Template identification, use of multiple templates and accounting for other environments (e.g. excluded ligand volumes), loop modelling, rotamer libraries for sidechain conformations, relaxation using MM forcefields.</td><td>Proprietary platform, supported on Windows, Linux and Mac</td></tr><tr><td><a href="/facts/Rosetta@home/IfxGBjNU">Robetta</a></td><td>Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction</td><td>Webserver</td></tr><tr><td><a href="/facts/Supercomputing_Facility_for_Bioinformatics_and_Computational_Biology/NDWfQ9yk">BHAGEERATH-H</a></td><td>Combination of ab initio folding and homology methods</td><td>Protein tertiary structure predictions</td></tr><tr><td><a href="/facts/Swiss-model/M9bFT2L9">Swiss-model</a></td><td>Local similarity/fragment assembly</td><td>Automated webserver (based on ProModII)</td></tr><tr><td><a href="/facts/Yasara/vof68M8J">Yasara</a></td><td>Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments</td><td>Graphical interface or text mode (clusters)</td></tr><tr><td>AWSEM-Suite</td><td><a href="/facts/Molecular_dynamics/yR3DNt6U">Molecular dynamics</a> simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes</td><td>Automated webserver</td></tr></tbody></table> <h3>Threading and fold recognition</h3> <p class="note">Main article: <a href="/facts/Protein_threading/Abv8Cvgy">Protein threading</a></p> <table><tbody><tr><th>Name</th><th>Method</th><th>Description</th><th>Release date</th></tr><tr><td>IntFOLD</td><td>A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues</td><td>Automated webserver and some downloadable programs</td></tr><tr><td><a href="/facts/RaptorX/dokKrRus">RaptorX</a></td><td>Remote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same group</td><td>Webserver with job manager, automatically updated fold library</td></tr><tr><td><a href="/facts/HH-suite/lIPBDAys">HHpred</a></td><td>Template detection, alignment, 3D modeling</td><td>Interactive webserver with help facility</td></tr><tr><td><a href="/facts/Phyre/0VX68zFv">Phyre</a>, Phyre2</td><td>Remote template detection, alignment, 3D modeling, multi-templates, <i>ab initio</i></td><td>Webserver with job manager, automatically updated fold library, genome searching and other facilities</td></tr><tr><td><a href="/facts/I-TASSER/7I0wLykq">I-TASSER</a></td><td>Threading fragment structure reassembly</td><td>On-line server for protein modeling</td></tr></tbody></table> <h3><i>Ab initio</i> structure prediction</h3> <p class="note">Main article: <a href="/facts/De_novo_protein_structure_prediction/vsqAt3gb">De novo protein structure prediction</a></p> <table><tbody><tr><th>Name</th><th>Method</th><th>Description</th><th>Release date</th></tr><tr><td>trRosetta</td><td>trRosetta is an algorithm for fast and accurate protein structure prediction. It supports single-sequence structure prediction with trRosettaX-Single.</td><td>Webserver and source codes available at: <a href="https://yanglab.qd.sdu.edu.cn/trRosetta/">https://yanglab.qd.sdu.edu.cn/trRosetta/</a></td></tr><tr><td><a href="/facts/Rosetta@home/IfxGBjNU">ROBETTA</a></td><td>Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction</td><td>Webserver</td></tr><tr><td><a href="/facts/Rosetta@home/IfxGBjNU">Rosetta@home</a></td><td>Distributed-computing implementation of Rosetta algorithm</td><td>Downloadable program</td></tr><tr><td><a href="/facts/Abalone_(molecular_mechanics)/q6qwJTp1">Abalone</a></td><td>Molecular Dynamics folding</td><td>Program</td></tr><tr><td>C-QUARK</td><td>C-QUARK is a method for <i>ab initio</i> protein structure prediction. Based on deep-learning based contact-map predictions into the fragment assembly simulations.</td><td>Webserver</td></tr></tbody></table> <h3>Secondary structure prediction</h3> <p class="note">Main article: <a href="/facts/Protein_structure_prediction/sj6AbLjI">Protein structure prediction § Secondary structure</a></p> <p>Detailed list of programs can be found at <a href="/facts/List_of_protein_secondary_structure_prediction_programs/wl1EUtgv">List of protein secondary structure prediction programs</a> </p> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/List_of_protein_secondary_structure_prediction_programs/wl1EUtgv">List of protein secondary structure prediction programs</a></li> <li><a href="/facts/Comparison_of_nucleic_acid_simulation_software/rn3ftAtp">Comparison of nucleic acid simulation software</a></li> <li><a href="/facts/List_of_software_for_molecular_mechanics_modeling/RabeF7vR">List of software for molecular mechanics modeling</a></li> <li><a href="/facts/Molecular_design_software/BsLuzcbr">Molecular design software</a></li> <li><a href="/facts/Protein_design/jFKIHFvc">Protein design</a></li> <li><a href="/facts/AlphaFold/DwBhppKC">AlphaFold</a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="https://bio.tools">bio.tools</a>, finding more tools</li></ul>