List of protein structure prediction software

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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[edit]

Main article: Homology modeling
Name Method Description Link
RaptorX remote homology detection, protein 3D modeling, binding site prediction Automated webserver and Downloadable program server and download
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[edit]

Main article: Protein threading
Name Method Description Link
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
SPARKS-X 3D structure modeling by Fold recognition according to Sequence profiles and structural profiles Webserver Server

Ab initio structure prediction[edit]

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
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[edit]

Name Method Description Link
RaptorX-SS8 predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles Webserver/downloadable server download
NetSurfP Profile-based neural network Webserver/downloadable server
GOR Information theory/Bayesian inference Many implementations Basic GOR GOR V
Jpred Neural network assignment Webserver server
Meta-PP Consensus prediction of other servers Webserver server
PREDATOR Knowledge-based database comparison Webserver server
PredictProtein Profile-based neural network Webserver server
PSIPRED two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST Webserver server
SymPred an improved dictionary based approach which captures local sequence similarities in a group of proteins Webserver server
YASSPP Cascaded SVM-based predictor using PSI-BLAST profiles Webserver server
PSSpred Multiple backpropagation neural network predictors from PSI-BLAST profiles Webserver/downloadable program server and downloadable program

Transmembrane helix prediction[edit]

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
SVMTop2 Support Vector Machines Webserver main page

Signal peptide prediction[edit]

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

See also[edit]