# 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.

## Software list

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

### Homology modeling

| Name | Method | Description |
| 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 |
| 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

| Name | Method | Description |
| 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

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