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List of protein structure prediction software

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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

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Main article: Protein structure prediction

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

Homology modeling

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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

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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

Ab initio structure prediction

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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

Secondary structure prediction

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Main article: Protein structure prediction § Secondary structure

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

See also

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References

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