Homology Modeling
| Name | Method | Description | Link |
|---|---|---|---|
| RaptorX | remote homology detection, accurate alignment, 3D modeling | Automated webserver | server |
| 3D-JIGSAW | Fragment assembly | Automated webserver | server |
| Biskit | wraps external programs into automated workflow | BLAST search, T-Coffee alignment, and MODELLER construction | project site |
| CABS | Reduced modeling tool | Downloadable program | download |
| CPHModel | Fragment assembly | Automated webserver | server |
| EasyModeller | GUI to MODELLER | Standalone windows executable | download |
| ESyPred3D | Template detection, alignment, 3D modeling | Automated webserver | server |
| FoldX | Energy calculations and protein design | Downloadable program | download |
| GeneSilico | Consensus template search/fragment assembly | Webserver | server |
| Geno3D | Satisfaction of spatial restraints | Automated webserver | server |
| HHpred | Template detection, alignment, 3D modeling | Interactive webserver with help facility | server download article |
| LIBRA I | LIght Balance for Remote Analogous proteins, ver. I | Webserver | server |
| LOMETS | Local Meta threading server | Meta-server combining 9 different programs | Server
download |
| MODELLER | Satisfaction of spatial restraints | Standalone program mainly in Fortran and Python | download Server |
| 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 | server |
| Prime | Physics-based energy function | Graphical interface, sequence alignment, secondary structure prediction, homology modeling, protein refinement, loop-prediction, and side-chain prediction | Download |
| Protinfo CM | Comparative modelling of protein structure using minimum perturbation and loop building | Web server | server |
| ROBETTA | Rosetta homology modeling and ab initio fragment assembly with Ginzu domain prediction | Webserver | server |
| BHAGEERATH-H | Combination of ab initio folding and homology methods | Protein tertiary structure predictions | server |
| Selvita Protein Modeling Platform | Package of tools for protein modeling | Free demo, interactive webserver and standalone program including: BLAST search, CABS modeling, 3D threading, Psi-Pred secondary structure prediction | Home page |
| SWISS-MODEL | Local similarity/fragment assembly | Automated webserver (based on ProModII) | server |
| TIP-STRUCTFAST | Automated Comparative Modeling | Webserver and knowledgebase | server |
| WHAT IF | Position specific rotamers | Standalone program and webinterface | Home page Webinterface |
| YASARA | Detection of templates, alignment, modeling incl. ligands and oligomers, hybridization of model fragments | Graphical interface or text mode (clusters) | Home page CASP8 results |
Read more about this topic: List Of Protein Structure Prediction Software
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