List of protein structure prediction software

This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.

Software list

Below is a list which separates programs according to the method used for structure prediction.

Homology modeling

Name Method Description Release dateReferenceIntFOLDA unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residuesAutomated webserver and some downloadable programs2011Roche & McGuffin, 2011 RaptorX remote homology detection, protein 3D modeling, binding site prediction Automated webserver and Downloadable program2011Peng & Xu, 2011 Biskit wraps external programs into automated workflow BLAST search, T-Coffee alignment, and MODELLER construction2007Grünberg et al., 2007ESyPred3D Template detection, alignment, 3D modeling Automated webserver2002Lambert et al., 2002 FoldX Energy calculations and protein design Downloadable program2005Schymkowitz et al., 2005 Phyre, Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities2009Kelley & Sternberg, 2009HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility2005Söding et al., 2005 MODELLER Satisfaction of spatial restraints Standalone program mainly in Fortran and Python1993Šali & Blundell, 1993 CONFOLD Satisfaction of contact and distance restraints Standalone program mainly in Fortran and Perl2015Adhikari et al., 2015 Molecular Operating Environment (MOE) 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. Proprietary platform, supported on Windows, Linux and Mac1994Chemical Computing Group; MOE documentation Robetta Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction Webserver2004Kim et al., 2004 BHAGEERATH-H Combination of ab initio folding and homology methods Protein tertiary structure predictions2014Jayaram et al., 2014 Swiss-model Local similarity/fragment assembly Automated webserver (based on ProModII)1993Peitsch et al.; SWISS-MODEL documentation Yasara Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments Graphical interface or text mode (clusters)2003YASARA development history/documentationAWSEM-Suite Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes Automated webserver2020Jin et al., 2020ModPipeAutomated comparative modeling; MODELLER-basedAutomated pipeline for large-scale comparative protein structure modeling using sequence–structure relationships and MODELLER-based model generation2003Eswar et al., 2003ModWebAutomated comparative modelingWeb-based automated comparative-modeling server that uses sequence searches, template selection, alignment and MODELLER for protein structure modeling2003Eswar et al.; ModWeb documentationCPHmodelsHomology modeling / fragment assemblyAutomated server for protein homology modeling using template identification, sequence–structure alignment and model construction2003Nielsen et al., 20033D-JIGSAWComparative modeling / rigid-body assemblyAutomated protein comparative-modeling server that identifies structural templates and assembles models from conserved structural regions2001Bates et al., 2001M4TMultiple-template comparative modelingComparative-modeling server that combines multiple templates with iterative optimization of alternative target–template alignments2005Fernandez-Fuentes et al., 2005ICMTemplate-based comparative modelingMolecular-modeling platform supporting protein homology modeling, template selection, alignment, loop modeling and structure refinement1994Abagyan et al. 2012; comparative modeling evaluationsPrimeComparative/homology modelingProtein-structure modeling module using template-based modeling, loop prediction and structural refinement2006Comparative modeling evaluationCOMPOSERRigid-body comparative modelingClassical comparative-modeling program that constructs protein models through rigid-body assembly of conserved structural regions1987Sutcliffe et al., 1987; comparative-modeling literaturePrISMComparative modeling / structural alignmentProtein modeling system that uses structural templates and sequence–structure relationships for comparative model construction.2000Yang & Honig; comparative-modeling literatureGeno3DHomology modeling / segment matchingWeb-based protein structure-prediction server that uses comparative modeling and structural template information to construct three-dimensional models.Combet et al., 2005

Threading and fold recognition

Name Method Description Release dateReference IntFOLD A unified interface for: Tertiary structure prediction/3D modelling, 3D model quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues Automated webserver and some downloadable programs2011Roche et al. (2011) RaptorX 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 Webserver with job manager, automatically updated fold library2011Peng & Xu (2011) HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility2005Söding, Biegert & Lupas (2005) Phyre, Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities2009Kelley & Sternberg (2009) I-TASSER Threading fragment structure reassemblyOn-line server for protein modeling https://zhanggroup.org/I-TASSER/2008Zhang (2008)

Ab initio structure prediction

Name Method Description Release dateReference trRosetta trRosetta is an algorithm for fast and accurate protein structure prediction. It supports single-sequence structure prediction with trRosettaX-Single. Webserver and source codes available at: https://yanglab.qd.sdu.edu.cn/trRosetta/2020Yang et al. (2020) ROBETTA Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction Webserver2004Kim, Chivian & Baker (2004) Rosetta@home Distributed-computing implementation of Rosetta algorithm Downloadable program2005Rosetta Commons timeline; Rosetta@home documentation Abalone Molecular Dynamics folding Program2006Abalone software documentationC-QUARKC-QUARK is a method for ab initio protein structure prediction. Based on deep-learning based contact-map predictions into the fragment assembly simulations.Webserver https://zhanggroup.org/C-QUARK/2021Zheng et al. (2021)AlphaFold2An end-to-end deep learning framework for protein structure predictionWebserver and downloadable program2021Jumper et al. (2021)D-I-TASSERThe deep learning-based I-TASSER program reportedly outperforms both AlphaFold2 and AlphaFold3Webserver https://zhanggroup.org/D-I-TASSER/2023Zheng et al. (2023)

Secondary structure prediction

Detailed list of programs can be found at List of protein secondary structure prediction programs

See also List of protein secondary structure prediction programs Comparison of nucleic acid simulation software List of software for molecular mechanics modeling Molecular design software Protein design AlphaFold

External links bio.tools, finding more tools

References