This list of protein structure prediction software summarizes commonly 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.
Homology modeling
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RaptorX | remote homology detection, accurate alignment, 3D modeling | Automated webserver | server |
3D-JIGSAW | Fragment assembly | Automated webserver | server |
Biskit | wraps external programs into automated workflow | BLAST search, T-Coffee alignment, and MODELLER construction | project site |
CABS | Reduced modeling tool | Downloadable program | download |
CPHModel | Fragment assembly | Automated webserver | server |
EasyModeller | GUI to MODELLER | Standalone windows executable | download |
ESyPred3D | Template detection, alignment, 3D modeling | Automated webserver | server |
FoldX | Energy calculations and protein design | Downloadable program | download |
GeneSilico | Consensus template search/fragment assembly | Webserver | server |
Geno3D | Satisfaction of spatial restraints | Automated webserver | server |
HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
LIBRA I | LIght Balance for Remote Analogous proteins, ver. I | Webserver | server |
LOMETS | Local Meta threading server | Meta-server combining 9 different programs | Server download |
MODELLER | Satisfaction of spatial restraints | Standalone program mainly in Fortran and Python | download Server |
Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
Prime | Physics-based energy function | Graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction | Download |
Protinfo CM | Comparative modelling of protein structure using minimum perturbation and loop building | Web server | server |
ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
BHAGEERATH-H | Combination of ab initio folding and homology methods | Protein tertiary structure predictions | server |
Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction | Home page |
SWISS-MODEL | Local similarity/fragment assembly | Automated webserver (based on ProModII) | server |
TIP-STRUCTFAST | Automated Comparative Modeling | Webserver and knowledgebase | server |
WHAT IF | Position specific rotamers | Standalone program and webinterface | Home page Webinterface |
YASARA | Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments | Graphical interface or text mode (clusters) | Home page CASP8 results |
Threading/fold recognition
Name | Method | Description | Link |
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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 | download server |
3D-PSSM | 3D-1D sequence profiling (replaced by Phyre) | Webserver | server |
Bioingbu | Evolutionary information recognition | Webserver | server |
HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
I-TASSER | Combination of ab initio folding and threading methods | Structural and function predictions | server download |
LOOPP | Multiple methods | Webserver | server |
mGenTHREADER/GenTHREADER | Sequence profile and predicted secondary structure | Webserver | main page |
MUSTER | profile-profile alignment | Webserver | server download |
Phyre and Phyre2 | Remote template detection, alignment, 3D modeling, multi-templates, ab initio | Webserver with job manager, automatically updated fold library, genome searching and other facilities | server |
RAPTOR | Integer programming based fold recognition | Free demo | download articles |
Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: 3D threading and flexible 3d threading | Home page |
SUPERFAMILY | Hidden Markov modeling | Webserver/standalone | main page |
SPARKSx/SP series | 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles | Webserver | Server |
Ab initio structure prediction
Main article: De novo protein structure prediction
Name | Method | Description | Link |
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QUARK | Monte Carlo fragment assembly | On-line server for protein modeling (best for ab initio folding in CASP9) | Server |
I-TASSER | Threading fragement structure reassembly | On-line server for protein modeling | Server download |
Selvita Protein Modeling Platform | Package of tools for protein modeling | Interactive webserver and standalone program including: CABS ab initio modeling | Home page |
ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
Rosetta@home | Distributed-computing implementation of Rosetta algorithm | Downloadable program | main page |
CABS | Reduced modeling tool | Downloadable program | download |
Bhageerath | A computational protocol for modeling and predicting protein structures at the atomic level. | Webserver | Server |
Abalone | Molecular Dynamics folding | Program | Example |
PEP-FOLD | De novo approach, based on a HMM structural alphabet | On-line server for peptide structure prediction | Server |
Secondary structure prediction
Transmembrane helix prediction
Main article: Transmembrane helix prediction
Signal peptide prediction
Name | Method | Description | Link |
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SignalP | artificial neural networks and hidden Markov models | Webserver/standalone | server |
See also