Biology:List of protein structure prediction software

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Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure.

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

Main article: Biology:Protein structure prediction

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

Homology modeling

Main article: Biology:Homology modeling
Name Method Description Release date Reference
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 programs 2011 Roche & McGuffin, 2011[1]
RaptorX remote homology detection, protein 3D modeling, binding site prediction Automated webserver and Downloadable program 2011 Peng & Xu, 2011[2]
Biskit wraps external programs into automated workflow BLAST search, T-Coffee alignment, and MODELLER construction 2007 Grünberg et al., 2007[3]
ESyPred3D Template detection, alignment, 3D modeling Automated webserver 2002 Lambert et al., 2002[4]
FoldX Energy calculations and protein design Downloadable program 2005 Schymkowitz et al., 2005[5]
Phyre, Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities 2009 Kelley & Sternberg, 2009[6]
HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility 2005 Söding et al., 2005[7]
MODELLER Satisfaction of spatial restraints Standalone program mainly in Fortran and Python 1993 Šali & Blundell, 1993[8]
CONFOLD Satisfaction of contact and distance restraints Standalone program mainly in Fortran and Perl 2015 Adhikari et al., 2015[9]
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 Mac 1994 Chemical Computing Group; MOE documentation
Robetta Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction Webserver 2004 Kim et al., 2004[10]
BHAGEERATH-H Combination of ab initio folding and homology methods Protein tertiary structure predictions 2014 Jayaram et al., 2014[11]
Swiss-model Local similarity/fragment assembly Automated webserver (based on ProModII) 1993 Peitsch et al.; SWISS-MODEL documentation[12]
Yasara Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments Graphical interface or text mode (clusters) 2003 YASARA development history/documentation[13]
AWSEM-Suite Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes Automated webserver 2020 Jin et al., 2020[14]
ModPipe Automated comparative modeling; MODELLER-based Automated pipeline for large-scale comparative protein structure modeling using sequence–structure relationships and MODELLER-based model generation 2003 Eswar et al., 2003[15]
ModWeb Automated comparative modeling Web-based automated comparative-modeling server that uses sequence searches, template selection, alignment and MODELLER for protein structure modeling 2003 Eswar et al.; ModWeb documentation[16]
CPHmodels Homology modeling / fragment assembly Automated server for protein homology modeling using template identification, sequence–structure alignment and model construction 2003 Nielsen et al., 2003[17]
3D-JIGSAW Comparative modeling / rigid-body assembly Automated protein comparative-modeling server that identifies structural templates and assembles models from conserved structural regions 2001 Bates et al., 2001[18]
M4T Multiple-template comparative modeling Comparative-modeling server that combines multiple templates with iterative optimization of alternative target–template alignments 2005 Fernandez-Fuentes et al., 2005[19]
ICM Template-based comparative modeling Molecular-modeling platform supporting protein homology modeling, template selection, alignment, loop modeling and structure refinement 1994 Abagyan et al. 2012; comparative modeling evaluations[20]
Prime Comparative/homology modeling Protein-structure modeling module using template-based modeling, loop prediction and structural refinement 2006 Comparative modeling evaluation[21]
COMPOSER Rigid-body comparative modeling Classical comparative-modeling program that constructs protein models through rigid-body assembly of conserved structural regions 1987 Sutcliffe et al., 1987; comparative-modeling literature[22]
PrISM Comparative modeling / structural alignment Protein modeling system that uses structural templates and sequence–structure relationships for comparative model construction. 2000 Yang & Honig; comparative-modeling literature[23]
Geno3D Homology modeling / segment matching Web-based protein structure-prediction server that uses comparative modeling and structural template information to construct three-dimensional models. Combet et al., 2005[24]

Threading and fold recognition

Name Method Description Release date Reference
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 programs 2011 Roche et al. (2011)[25]
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 library 2011 Peng & Xu (2011)[26]
HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility 2005 Söding, Biegert & Lupas (2005)[27]
Phyre, Phyre2 Remote template detection, alignment, 3D modeling, multi-templates, ab initio Webserver with job manager, automatically updated fold library, genome searching and other facilities 2009 Kelley & Sternberg (2009)[28]
I-TASSER Threading fragment structure reassembly On-line server for protein modeling https://zhanggroup.org/I-TASSER/ 2008 Zhang (2008)[29]

Ab initio structure prediction

Main article: Biology:De novo protein structure prediction
Name Method Description Release date Reference
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/ 2020 Yang et al. (2020)[30]
ROBETTA Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction Webserver 2004 Kim, Chivian & Baker (2004)[31]
Rosetta@home Distributed-computing implementation of Rosetta algorithm Downloadable program 2005 Rosetta Commons timeline; Rosetta@home documentation
Abalone Molecular Dynamics folding Program 2006 Abalone software documentation[32]
C-QUARK C-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/ 2021 Zheng et al. (2021)[33]
AlphaFold2 An end-to-end deep learning framework for protein structure prediction Webserver and downloadable program 2021 Jumper et al. (2021)[34]
D-I-TASSER The deep learning-based I-TASSER program reportedly outperforms both AlphaFold2 and AlphaFold3 Webserver https://zhanggroup.org/D-I-TASSER/ 2023 Zheng et al. (2023)[35]

Secondary structure prediction

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

See also

References

  1. ↑ Roche, Daniel B.; Buenavista, Maria T.; Tetchner, Stuart J.; McGuffin, Liam J. (2011-07-01). "The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction". Nucleic Acids Research 39 (suppl_2): W171–W176. doi:10.1093/nar/gkr184. ISSN 0305-1048. PMID 21459847. PMC 3125722. https://doi.org/10.1093/nar/gkr184. 
  2. ↑ Peng, Jian; Xu, Jinbo (2011). "Raptorx: Exploiting structure information for protein alignment by statistical inference" (in en). Proteins: Structure, Function, and Bioinformatics 79 (S10): 161–171. doi:10.1002/prot.23175. ISSN 1097-0134. PMID 21987485. 
  3. ↑ Grünberg, Raik; Nilges, Michael; Leckner, Johan (2007-03-01). "Biskit—A software platform for structural bioinformatics". Bioinformatics 23 (6): 769–770. doi:10.1093/bioinformatics/btl655. ISSN 1367-4803. PMID 17237072. https://doi.org/10.1093/bioinformatics/btl655. 
  4. ↑ Lambert, Christophe; Léonard, Nadia; De Bolle, Xavier; Depiereux, Eric (2002-09-01). "ESyPred3D: Prediction of proteins 3D structures". Bioinformatics 18 (9): 1250–1256. doi:10.1093/bioinformatics/18.9.1250. ISSN 1367-4803. PMID 12217917. https://doi.org/10.1093/bioinformatics/18.9.1250. 
  5. ↑ Schymkowitz, Joost; Borg, Jesper; Stricher, Francois; Nys, Robby; Rousseau, Frederic; Serrano, Luis (2005-07-01). "The FoldX web server: an online force field". Nucleic Acids Research 33 (suppl_2): W382–W388. doi:10.1093/nar/gki387. ISSN 0305-1048. PMID 15980494. PMC 1160148. https://doi.org/10.1093/nar/gki387. 
  6. ↑ Kelley, Lawrence A.; Sternberg, Michael J. E. (March 2009). "Protein structure prediction on the Web: a case study using the Phyre server" (in en). Nature Protocols (Nature Publishing Group) 4 (3): 363–371. doi:10.1038/nprot.2009.2. ISSN 1750-2799. PMID 19247286. https://www.nature.com/articles/nprot.2009.2. 
  7. ↑ Söding, Johannes; Biegert, Andreas; Lupas, Andrei N. (2005-07-01). "The HHpred interactive server for protein homology detection and structure prediction". Nucleic Acids Research 33 (suppl_2): W244–W248. doi:10.1093/nar/gki408. ISSN 0305-1048. PMID 15980461. PMC 1160169. https://doi.org/10.1093/nar/gki408. 
  8. ↑ Webb, Benjamin; Sali, Andrej (2016). "Comparative Protein Structure Modeling Using MODELLER" (in en). Current Protocols in Bioinformatics 54 (1): 5.6.1–5.6.37. doi:10.1002/cpbi.3. ISSN 1934-340X. PMID 27322406. 
  9. ↑ Adhikari, Badri; Bhattacharya, Debswapna; Cao, Renzhi; Cheng, Jianlin (August 2015). "CONFOLD: Residue-residue contact-guided ab initio protein folding: Contact-Guided Protein Folding" (in en). Proteins: Structure, Function, and Bioinformatics 83 (8): 1436–1449. doi:10.1002/prot.24829. PMID 25974172. 
  10. ↑ Kim, David E.; Chivian, Dylan; Baker, David (2004-07-01). "Protein structure prediction and analysis using the Robetta server". Nucleic Acids Research 32 (suppl_2): W526–W531. doi:10.1093/nar/gkh468. ISSN 0305-1048. PMID 15215442. PMC 441606. https://doi.org/10.1093/nar/gkh468. 
  11. ↑ Jayaram, B.; Dhingra, Priyanka; Mishra, Avinash; Kaushik, Rahul; Mukherjee, Goutam; Singh, Ankita; Shekhar, Shashank (2014-12-08). "Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins". BMC Bioinformatics 15 (16): S7. doi:10.1186/1471-2105-15-S16-S7. ISSN 1471-2105. PMID 25521245. 
  12. ↑ Schwede, Torsten; Kopp, Jürgen; Guex, Nicolas; Peitsch, Manuel C. (2003-07-01). "SWISS-MODEL: an automated protein homology-modeling server". Nucleic Acids Research 31 (13): 3381–3385. doi:10.1093/nar/gkg520. ISSN 0305-1048. PMID 12824332. PMC 168927. https://doi.org/10.1093/nar/gkg520. 
  13. ↑ "YASARA - Yet Another Scientific Artificial Reality Application". https://www.yasara.org/index.html. 
  14. ↑ Jin, Shikai; Contessoto, Vinicius G; Chen, Mingchen; Schafer, Nicholas P; Lu, Wei; Chen, Xun; Bueno, Carlos; Hajitaheri, Arya et al. (2020-07-02). "AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes". Nucleic Acids Research 48 (W1): W25–W30. doi:10.1093/nar/gkaa356. ISSN 0305-1048. PMID 32383764. PMC 7319565. https://doi.org/10.1093/nar/gkaa356. 
  15. ↑ Schwede, Torsten; Kopp, Jürgen; Guex, Nicolas; Peitsch, Manuel C. (2003-07-01). "SWISS-MODEL: an automated protein homology-modeling server". Nucleic Acids Research 31 (13): 3381–3385. doi:10.1093/nar/gkg520. ISSN 0305-1048. PMID 12824332. PMC 168927. https://doi.org/10.1093/nar/gkg520. 
  16. ↑ "References | SWISS-MODEL" (in en). https://swissmodel.expasy.org/docs/references. 
  17. ↑ Schwede, Torsten; Kopp, Jürgen; Guex, Nicolas; Peitsch, Manuel C. (2003-07-01). "SWISS-MODEL: an automated protein homology-modeling server". Nucleic Acids Research 31 (13): 3381–3385. doi:10.1093/nar/gkg520. ISSN 0305-1048. PMID 12824332. PMC 168927. https://doi.org/10.1093/nar/gkg520. 
  18. ↑ Schwede, Torsten; Kopp, Jürgen; Guex, Nicolas; Peitsch, Manuel C. (2003-07-01). "SWISS-MODEL: an automated protein homology-modeling server". Nucleic Acids Research 31 (13): 3381–3385. doi:10.1093/nar/gkg520. ISSN 0305-1048. PMID 12824332. PMC 168927. https://doi.org/10.1093/nar/gkg520. 
  19. ↑ "Appendix B: Modelling Services | SWISS-MODEL". https://swissmodel.expasy.org/coursetext/appendix_B.htm?. 
  20. ↑ Dolan, Michael A.; Noah, James W.; Hurt, Darrell (2012), Orry, Andrew J. W.; Abagyan, Ruben, eds., "Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments", Homology Modeling: Methods and Protocols (Totowa, NJ: Humana Press) 857: pp. 399–414, doi:10.1007/978-1-61779-588-6_18, ISBN 978-1-61779-588-6, PMID 22323232, https://doi.org/10.1007/978-1-61779-588-6_18, retrieved 2026-09-14 
  21. ↑ Dolan, Michael A.; Noah, James W.; Hurt, Darrell (2012), Orry, Andrew J. W.; Abagyan, Ruben, eds., "Comparison of Common Homology Modeling Algorithms: Application of User-Defined Alignments", Homology Modeling: Methods and Protocols (Totowa, NJ: Humana Press) 857: pp. 399–414, doi:10.1007/978-1-61779-588-6_18, ISBN 978-1-61779-588-6, PMID 22323232, https://doi.org/10.1007/978-1-61779-588-6_18, retrieved 2026-09-14 
  22. ↑ Xiang, Zhexin (2012-03-01). "Advances in Homology Protein Structure Modeling" (in en). Current Protein & Peptide Science 7 (3): 217–227. doi:10.2174/138920306777452312. PMID 16787261. PMC 1839925. https://www.eurekaselect.com/article/2109. 
  23. ↑ "Error: no |title= specified when using {{Cite web}}" (in en). https://www.salilab.org/publication-archive/Fiser_CompBioChemPhys_2000.pdf?. 
  24. ↑ "1. Introduction". https://paperzz.com/doc/7139041/1.-introduction. 
  25. ↑ Roche, Daniel B.; Buenavista, Maria T.; Tetchner, Stuart J.; McGuffin, Liam J. (2011-07-01). "The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction". Nucleic Acids Research 39 (suppl_2): W171–W176. doi:10.1093/nar/gkr184. ISSN 0305-1048. PMID 21459847. PMC 3125722. https://doi.org/10.1093/nar/gkr184. 
  26. ↑ Peng, Jian; Xu, Jinbo (2011). "Raptorx: Exploiting structure information for protein alignment by statistical inference" (in en). Proteins: Structure, Function, and Bioinformatics 79 (S10): 161–171. doi:10.1002/prot.23175. ISSN 1097-0134. PMID 21987485. 
  27. ↑ Söding, Johannes; Biegert, Andreas; Lupas, Andrei N. (2005-07-01). "The HHpred interactive server for protein homology detection and structure prediction". Nucleic Acids Research 33 (suppl_2): W244–W248. doi:10.1093/nar/gki408. ISSN 0305-1048. PMID 15980461. PMC 1160169. https://doi.org/10.1093/nar/gki408. 
  28. ↑ Kelley, Lawrence A.; Sternberg, Michael J. E. (March 2009). "Protein structure prediction on the Web: a case study using the Phyre server" (in en). Nature Protocols (Nature Publishing Group) 4 (3): 363–371. doi:10.1038/nprot.2009.2. ISSN 1750-2799. PMID 19247286. https://www.nature.com/articles/nprot.2009.2. 
  29. ↑ Zhang, Yang (2008-01-23). "I-TASSER server for protein 3D structure prediction". BMC Bioinformatics 9 (1). doi:10.1186/1471-2105-9-40. ISSN 1471-2105. PMID 18215316. 
  30. ↑ Du, Zongyang; Su, Hong; Wang, Wenkai; Ye, Lisha; Wei, Hong; Peng, Zhenling; Anishchenko, Ivan; Baker, David et al. (December 2021). "The trRosetta server for fast and accurate protein structure prediction" (in en). Nature Protocols (Nature Publishing Group) 16 (12): 5634–5651. doi:10.1038/s41596-021-00628-9. ISSN 1750-2799. PMID 34759384. https://www.nature.com/articles/s41596-021-00628-9. 
  31. ↑ Kim, David E.; Chivian, Dylan; Baker, David (2004-07-01). "Protein structure prediction and analysis using the Robetta server". Nucleic Acids Research 32 (suppl_2): W526–W531. doi:10.1093/nar/gkh468. ISSN 0305-1048. PMID 15215442. PMC 441606. https://doi.org/10.1093/nar/gkh468. 
  32. ↑ "Molecular simulations with Abalone-II". https://www.biomolecular-modeling.com/Abalone/Simulations.html?. 
  33. ↑ Mortuza, S. M.; Zheng, Wei; Zhang, Chengxin; Li, Yang; Pearce, Robin; Zhang, Yang (2021-08-18). "Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions" (in en). Nature Communications (Nature Publishing Group) 12 (1): 5011. doi:10.1038/s41467-021-25316-w. ISSN 2041-1723. PMID 34408149. Bibcode: 2021NatCo..12.5011M. 
  34. ↑ Jumper, John; Evans, Richard; Pritzel, Alexander; Green, Tim; Figurnov, Michael; Ronneberger, Olaf; Tunyasuvunakool, Kathryn; Bates, Russ et al. (August 2021). "Highly accurate protein structure prediction with AlphaFold" (in en). Nature (Nature Publishing Group) 596 (7873): 583–589. doi:10.1038/s41586-021-03819-2. ISSN 1476-4687. PMID 34265844. Bibcode: 2021Natur.596..583J. 
  35. ↑ Zheng, Wei; Wuyun, Qiqige; Freddolino, Lydia; Zhang, Yang (2023). "Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15" (in en). Proteins: Structure, Function, and Bioinformatics 91 (12): 1684–1703. doi:10.1002/prot.26585. ISSN 1097-0134. PMID 37650367. 



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