Summary of Protein 3D Structure Prediction Software
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| Homology Modeling | Software | Method | Description |
| AWSEM-Suite | Molecular dynamics simulation based on template-guided, coevolutionary-enhanced optimized folding landscapes | Automated webserver | |
| BHAGEERA TH-H | Combination of ab initio folding and homology methods | Protein tertiary structure predictions | |
| Biskit | Wraps external programs into an automated workflow | BLAST search, T-Coffee alignment, and MODE LLER construction | |
| CONFOLD | Satisfaction of contact and distance restraints | The standalone program mainly in Fortran and Perl | |
| ESyPred 3D | Template detection, alignment, 3D modeling | Automated webserver | |
| FoldX | Energy calculations and protein design | Downloadable programs | |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | |
| IntFOLD | A unified interface for Tertiary structure prediction/3D modeling, 3D models quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues | Automated web server and some downloadable programs | |
| MODELLER | Satisfaction of spatial restraints | The standalone program mainly in Fortran and Python | |
| MOE | Template identification, use of multiple templates and accounting for other environments (e.g., excluded ligand volumes), loop modeling, rotamer libraries for sidechain conformations, and relaxation using MM forcefields. | Proprietary platform, supported on Windows, Linux, and Mac | |
| 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 | |
| RaptorX | Remote homology detection, protein 3D modeling, binding site prediction | Automated web server and downloadable programs | |
| Robetta | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | |
| SWISS-MODEL | Local similarity/fragment assembly | Automated web server (based on ProModll) | |
| Yasara | Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments | Graphical interface or text mode (clusters) | |
| Threading/Fold Recognition | IntFOLD | A unified interface for Tertiary structure prediction/3D modeling, 3D models quality assessment, Intrinsic disorder prediction, Domain prediction, Prediction of protein-ligand binding residues | Automated web server and some downloadable programs |
| I-TASSER | Threading fragment structure reassembly | Online server for protein modeling | |
| 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 | |
| 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 | |
| Ab initio Structure Prediction | 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 | |
| Robetta | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | |
| Robetta@home | Distributed-computing implementation of Rosetta algorithm | Downloadable program | |
| trRosetta | 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 |
Creative Biostructure has been working in the field of structural biology, membrane protein technologies, and structure-based drug discovery. We have expertise and experience in protein 3D structure prediction, protein modeling, and data analysis. Feel free to discuss your research project with our experts.
