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.

Homology modeling

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

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
SPARKSx/SP series	3D structure modeling by Fold recognition according to Sequence profiles and structural profiles	Webserver	Server

Ab initio structure prediction

Main article: De novo protein 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
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

Main article: Protein structure prediction#Secondary_structure

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	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	main page
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

Main article: 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
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

• List of nucleic acid simulation software
• List of software for molecular mechanics modeling
• Molecular design software
• Protein design