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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.

Contents

Software listEdit

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

Homology modelingEdit

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

download

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 recognitionEdit

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

download

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
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

download

Ab initio structure predictionEdit

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

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
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 predictionEdit

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

Transmembrane helix predictionEdit

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 predictionEdit

Name Method Description Link
SignalP artificial neural networks and hidden Markov models Webserver/standalone server

See alsoEdit

ReferencesEdit