List of protein structure prediction software

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

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.

Software list[]

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

Homology modeling[]

Name	Method	Description	Link
	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
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
	Satisfaction of contact and distance restraints	Standalone program mainly in Fortran and Perl	download
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
	Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes^[1]	Automated webserver	server

Threading/fold recognition[]

Name	Method	Description	Link
	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
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 prediction[]

Name	Method	Description	Link
	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 neural 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 prediction[]

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

External link[]

bio.tools, finding more tools

References[]

^ Jin, Shikai; Contessoto, Vinicius G; Chen, Mingchen; Schafer, Nicholas P; Lu, Wei; Chen, Xun; Bueno, Carlos; Hajitaheri, Arya; Sirovetz, Brian J; Davtyan, Aram; Papoian, Garegin A; Tsai, Min-Yeh; Wolynes, Peter G (2 July 2020). "AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes". Nucleic Acids Research. 48 (W1): W25–W30. doi:10.1093/nar/gkaa356. PMC 7319565. PMID 32383764.

[1] Jin, Shikai; Contessoto, Vinicius G; Chen, Mingchen; Schafer, Nicholas P; Lu, Wei; Chen, Xun; Bueno, Carlos; Hajitaheri, Arya; Sirovetz, Brian J; Davtyan, Aram; Papoian, Garegin A; Tsai, Min-Yeh; Wolynes, Peter G (2 July 2020). "AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes". Nucleic Acids Research. 48 (W1): W25–W30. doi:10.1093/nar/gkaa356. PMC 7319565. PMID 32383764.

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