List of protein structure prediction software

This list of protein structure prediction software summarizes notable 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.

Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure.

Software listEdit

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

Homology modelingEdit

Name Method Description Link
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
ESyPred3D Template detection, alignment, 3D modeling Automated webserver server
FoldX Energy calculations and protein design Downloadable program 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
HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility server download article
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
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
SWISS-MODEL Local similarity/fragment assembly Automated webserver (based on ProModII) server
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
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
HHpred Template detection, alignment, 3D modeling Interactive webserver with help facility server download article
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

Ab initio structure predictionEdit

Name Method Description Link
trRosetta trRosetta is an algorithm for fast and accurate de novo protein structure prediction. It builds the protein structure based on direct energy minimizations with a restrained Rosetta. The restraints include inter-residue distance and orientation distributions, predicted by a deep residual nerual network. Webserver and source codes. It takes about one hour to fold proteins with ~300 AAs Server

download

I-TASSER Threading fragment structure reassembly On-line server for protein modeling Server

download

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
Abalone Molecular Dynamics folding Program Example

Secondary structure predictionEdit

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

See alsoEdit

ReferencesEdit