List of protein structure prediction software

Short description: none

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.

## Contents

* 1 Software list
* 1.1 Homology modeling
* 1.2 Threading and fold recognition
* 1.3 Ab initio structure prediction
* 1.4 Secondary structure prediction
* 2 See also
* 3 External links
* 4 References

## Software list

Main article: Biology:Protein structure prediction

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

### Homology modeling

Main article: Biology: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

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: Biology: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

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

## References

* v
* t
* e

Computer simulation software

Biology|

* Protein structure prediction
* Nucleic acid simulation

Chemistry|

* Quantum chemistry
* Molecular modeling
* Monte Carlo molecular modeling
* Molecular design

Physics|

* Finite element
* Cosmological simulation

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