List of protein structure prediction software
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.
Software list
Below is a list which separates programs according to the method used for structure prediction.
Homology modeling
Name | Method | Description | Link |
---|---|---|---|
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 | server and downloads |
RaptorX | remote homology detection, protein 3D modeling, binding site prediction | Automated webserver and Downloadable program | server and download |
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 |
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 |
Homology Modeling Professional for HyperChem | Template detection, alignment, secondary structure prediction, 3D modeling, ab initio loop modeling, energy-based side-chain rotamer prediction | Standalone windows executable | Home page |
LOMETS | Local Meta threading server | Meta-server combining 9 different programs | Server |
MODELLER | Satisfaction of spatial restraints | Standalone program mainly in Fortran and Python | download Server |
MOE (Molecular Operating Environment) | 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 | site |
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 | site |
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 |
STRUCTUROPEDIA | WebInterface to MODELLER | Homology modeling of proteins in monomeric or multimeric forms alone and in complex with peptides and DNA as well as introduction of mutations and post-translational modifications (PTMs) into protein structures | server |
SWISS-MODEL | Local similarity/fragment assembly | Automated webserver (based on ProModII) | server |
TIP-STRUCTFAST | Automated Comparative Modeling | Webserver | site |
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 |
---|---|---|---|
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 | server and downloads |
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 |
FALCON@home | Single-template and multi-template threading, a high-throughput server based on volunteer computing | Webserver with job manager | article server |
HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
I-TASSER | Combination of ab initio folding and threading methods | Structural and function predictions | server |
mGenTHREADER/GenTHREADER | Sequence profile and predicted secondary structure | Webserver | main page |
MUSTER | profile-profile alignment | Webserver | 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 |
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 |
SPARKS-X | 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles | Webserver | Server |
BBSP - Building Blocks Structure Predictor | Hybrid template-based | Free application plus database | main page |
DeepFR | Remote template selection, 3D modeling | Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts | server |
Ab initio structure prediction
Name | Method | Description | Link |
---|---|---|---|
EVfold | Evolutionary couplings calculated from correlated mutations in a protein family, used to predict 3D structure from sequences alone and to predict functional residues from coupling strengths. Predicts both globular and transmembrane proteins. | Webserver | Server |
FALCON | A position-specific hidden Markov model to predict protein structure by iteratively refining the distributions of dihedral angles | Webserver | article server |
QUARK | Monte Carlo fragment assembly | On-line server for protein modeling (best for ab initio folding in CASP9) | Server |
NovaFold | Combination of threading and ab initio folding | Commercial protein structure prediction application | Home page |
I-TASSER | Threading fragment structure reassembly | On-line server for protein modeling | Server |
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 |
CABS-FOLD | Server for de novo modeling, can also use alternative templates (consensus modeling). | Webserver | server |
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
Detailed list of programs can be found at List of protein secondary structure prediction programs
Transmembrane helix prediction
Name | Method | Description | Link |
---|---|---|---|
HMMTOP | Hidden Markov Model | Webserver/standalone | main page |
MEMSAT | Neural networks and SVMs | Webserver/standalone | main page |
PHDhtm in PredictProtein | Multiple alignment-based neural network system | Webserver/standalone | server |
Phobius | Homology supported predictions | Webserver/standalone | main page |
TMHMM | Hidden Markov Model | Webserver/standalone | main page |
CCTOP | Consensus/Hidden Markov Model | Webserver/standalone | main page |
SVMTop2 | Support Vector Machines | Webserver | main page |
Signal peptide prediction
Name | Method | Description | Link |
---|---|---|---|
SignalP | artificial neural networks and hidden Markov models | Webserver/standalone | server |
See also
References
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