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

NameMethodDescriptionLink
IntFOLDA 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 programs
RaptorXremote homology detection, protein 3D modeling, binding site predictionAutomated webserver and Downloadable program
Biskitwraps external programs into automated workflowBLAST search, T-Coffee alignment, and MODELLER construction
CABSReduced modeling toolDownloadable program
CPHModelFragment assemblyAutomated webserver
ESyPred3DTemplate detection, alignment, 3D modelingAutomated webserver
FoldXEnergy calculations and protein designDownloadable program
GeneSilicoConsensus template search/fragment assemblyWebserver
Geno3DSatisfaction of spatial restraintsAutomated webserver
HHpredTemplate detection, alignment, 3D modelingInteractive webserver with help facility
Homology Modeling Professional for HyperChemTemplate detection, alignment, secondary structure prediction, 3D modeling, ab initio loop modeling, energy-based side-chain rotamer predictionStandalone windows executable
LOMETSLocal Meta threading serverMeta-server combining 9 different programs
MODELLERSatisfaction of spatial restraintsStandalone program mainly in Fortran and Python
MOE Template identification, use of multiple templates and accounting for other environments, loop modelling, rotamer libraries for sidechain conformations, relaxation using MM forcefields.Proprietary platform, supported on Windows, Linux and Mac
Phyre and Phyre2Remote template detection, alignment, 3D modeling, multi-templates, ab initioWebserver with job manager, automatically updated fold library, genome searching and other facilities
PrimePhysics-based energy functionGraphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction
ROBETTARosetta homology modeling and ab initio fragment assembly with Ginzu domain predictionWebserver
BHAGEERATH-HCombination of ab initio folding and homology methodsProtein tertiary structure predictions
Selvita Protein Modeling PlatformPackage of tools for protein modelingFree demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction
STRUCTUROPEDIAWebInterface to MODELLERHomology 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 into protein structures
SWISS-MODELLocal similarity/fragment assemblyAutomated webserver
TIP-STRUCTFASTAutomated Comparative ModelingWebserver
WHAT IFPosition specific rotamersStandalone program and webinterface
YasaraDetection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragmentsGraphical interface or text mode

Threading/fold recognition

NameMethodDescriptionLink
IntFOLDA 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 programs
RaptorXRemote template detection, single-template and multi-template threading, totally different from and much better than the old program RAPTOR designed by the same groupWebserver with job manager, automatically updated fold library
FALCON@homeSingle-template and multi-template threading, a high-throughput server based on volunteer computingWebserver with job manager
HHpredTemplate detection, alignment, 3D modelingInteractive webserver with help facility
NovaFoldCombination of threading and ab initio foldingCommercial protein structure prediction application
I-TASSERCombination of ab initio folding and threading methodsStructural and function predictions
mGenTHREADER/GenTHREADERSequence profile and predicted secondary structureWebserver
MUSTERprofile-profile alignmentWebserver
Phyre and Phyre2Remote template detection, alignment, 3D modeling, multi-templates, ab initioWebserver with job manager, automatically updated fold library, genome searching and other facilities
Selvita Protein Modeling PlatformPackage of tools for protein modelingFree demo, interactive webserver and standalone program including: 3D threading and flexible 3d threading
SUPERFAMILYHidden Markov modelingWebserver/standalone
SPARKS-X3D structure modeling by Fold recognition according to Sequence profiles and structural profilesWebserver
BBSP - Building Blocks Structure PredictorHybrid template-basedFree application plus database
DeepFRRemote template selection, 3D modelingImproving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts

''Ab initio'' structure prediction

NameMethodDescriptionLink
trRosettatrRosetta is an algortihm for fast and accurate de novo protein structure prediction. It builds the structure by deep learning restraints-guided energy mimization in Rosetta.Webserver and standalone package
EVfoldEvolutionary 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
FALCONA position-specific hidden Markov model to predict protein structure by iteratively refining the distributions of dihedral anglesWebserver
QUARKMonte Carlo fragment assemblyOn-line server for protein modeling
NovaFoldCombination of threading and ab initio foldingCommercial protein structure prediction application
I-TASSERThreading fragment structure reassemblyOn-line server for protein modeling
Selvita Protein Modeling PlatformPackage of tools for protein modelingInteractive webserver and standalone program including: CABS ab initio modeling
ROBETTARosetta homology modeling and ab initio fragment assembly with Ginzu domain predictionWebserver
Rosetta@homeDistributed-computing implementation of Rosetta algorithmDownloadable program
CABSReduced modeling toolDownloadable program
CABS-FOLDServer for de novo modeling, can also use alternative templates.Webserver
BhageerathA computational protocol for modeling and predicting protein structures at the atomic level.Webserver
AbaloneMolecular Dynamics foldingProgram
PEP-FOLDDe novo approach, based on a HMM structural alphabetOn-line server for peptide structure prediction

Secondary structure prediction

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

Transmembrane helix prediction

NameMethodDescriptionLink
HMMTOPHidden Markov ModelWebserver/standalone
MEMSATNeural networks and SVMsWebserver/standalone
PHDhtm in PredictProteinMultiple alignment-based neural network systemWebserver/standalone
PhobiusHomology supported predictionsWebserver/standalone
TMHMMHidden Markov ModelWebserver/standalone
CCTOPConsensus/Hidden Markov ModelWebserver/standalone
SVMTop2Support Vector MachinesWebserver

Signal peptide prediction

NameMethodDescriptionLink
SignalPartificial neural networks and hidden Markov modelsWebserver/standalone
PhobiusWebserver