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 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 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 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 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 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 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

References

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