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 list

Main article: Protein structure prediction

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

Homology modeling

Main article: Homology modeling

Name	Method	Description	Release date
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
RaptorX	remote homology detection, protein 3D modeling, binding site prediction	Automated webserver and Downloadable program
Biskit	wraps external programs into automated workflow	BLAST search, T-Coffee alignment, and MODELLER construction
ESyPred3D	Template detection, alignment, 3D modeling	Automated webserver
FoldX	Energy calculations and protein design	Downloadable program
Phyre, Phyre2	Remote template detection, alignment, 3D modeling, multi-templates, ab initio	Webserver with job manager, automatically updated fold library, genome searching and other facilities
HHpred	Template detection, alignment, 3D modeling	Interactive webserver with help facility
MODELLER	Satisfaction of spatial restraints	Standalone program mainly in Fortran and Python
CONFOLD	Satisfaction of contact and distance restraints	Standalone program mainly in Fortran and Perl
Molecular Operating Environment (MOE)	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
Robetta	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction	Webserver
BHAGEERATH-H	Combination of ab initio folding and homology methods	Protein tertiary structure predictions
Swiss-model	Local similarity/fragment assembly	Automated webserver (based on ProModII)
Yasara	Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments	Graphical interface or text mode (clusters)
AWSEM-Suite	Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes	Automated webserver

Threading and fold recognition

Main article: Protein threading

Name	Method	Description	Release date
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
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
HHpred	Template detection, alignment, 3D modeling	Interactive webserver with help facility
Phyre, Phyre2	Remote template detection, alignment, 3D modeling, multi-templates, ab initio	Webserver with job manager, automatically updated fold library, genome searching and other facilities
I-TASSER	Threading fragment structure reassembly	On-line server for protein modeling https://zhanggroup.org/I-TASSER/

Ab initio structure prediction

Main article: De novo protein structure prediction

Name	Method	Description	Release date
trRosetta	trRosetta is an algorithm for fast and accurate protein structure prediction. It supports single-sequence structure prediction with trRosettaX-Single.	Webserver and source codes available at: https://yanglab.qd.sdu.edu.cn/trRosetta/
ROBETTA	Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction	Webserver
Rosetta@home	Distributed-computing implementation of Rosetta algorithm	Downloadable program
Abalone	Molecular Dynamics folding	Program
C-QUARK	C-QUARK is a method for ab initio protein structure prediction. Based on deep-learning based contact-map predictions into the fragment assembly simulations.	Webserver https://zhanggroup.org/C-QUARK/
AlphaFold2	An end-to-end deep learning framework for protein structure prediction	Webserver and downloadable program
D-I-TASSER	The deep learning-based I-TASSER program reportedly outperforms both AlphaFold2 and AlphaFold3	Webserver https://zhanggroup.org/D-I-TASSER/

Secondary structure prediction

Main article: Protein structure prediction § Secondary structure

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

See also

• List of protein secondary structure prediction programs
• Comparison of nucleic acid simulation software
• List of software for molecular mechanics modeling
• Molecular design software
• Protein design
• AlphaFold

External links

• bio.tools, finding more tools