| Multiple sequence alignment (MSA) construction |
| PSI-BLAST |
https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| HHBlits |
Web server- https://toolkit.tuebingen.mpg.de/tools/hhblits
Downloadable version -https://github.com/soedinglab/hh-suite
|
| Jackhmmer |
https://www.ebi.ac.uk/Tools/hmmer/search/jackhmmer |
| Hmmsearch |
https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch |
| DeepMSA |
https://zhanglab.ccmb.med.umich.edu/DeepMSA/ |
| Threading and Fold-recognition |
| LOMETS |
https://zhanglab.dcmb.med.umich.edu/LOMETS/ |
| HHsearch |
https://github.com/soedinglab/hh-suite |
| MUSTER |
https://zhanglab.dcmb.med.umich.edu/MUSTER/ |
| map_align |
https://github.com/sokrypton/map_align |
| EigenTHREADER |
https://github.com/psipred/eigenthreader |
| CEthreader |
https://zhanglab.dcmb.med.umich.edu/CEthreader/ |
| DisCovER |
https://github.com/Bhattacharya-Lab/DisCovER |
| RaptorX |
http://raptorx.uchicago.edu |
| Full-length Structure Assembly for Template-Based Modeling (TBM) |
| I-TASSER |
https://zhanglab.dcmb.med.umich.edu/I-TASSER/ |
| MODELLER |
https://salilab.org/modeller/ |
| RosettaCM |
https://www.rosettacommons.org/software/license-and-download |
| SWISS-MODEL |
https://swissmodel.expasy.org/ |
| Phyre2 |
http://www.sbg.bio.ic.ac.uk/phyre2/ |
| Fragment Assembly Simulation Methods for Free Modeling (FM) |
| Rosetta |
Web server: https://robetta.bakerlab.org
Downloadable version: https://www.rosettacommons.org/software/license-and-download
|
| QUARK |
https://zhanglab.dcmb.med.umich.edu/QUARK/ |
| FragFold |
https://github.com/psipred/fragfold |
| Co-evolution and Deep Learning-Based Contact/Distance Prediction |
| PSICOV |
http://bioinfadmin.cs.ucl.ac.uk/downloads/PSICOV/ |
| CCMpred |
https://github.com/soedinglab/CCMpred |
| GREMLIN |
http://gremlin.bakerlab.org |
| NeBcon |
https://zhanglab.dcmb.med.umich.edu/NeBcon/ |
| MetaPSICOV |
http://bioinf.cs.ucl.ac.uk/psipred/ |
| ResPRE |
https://zhanglab.dcmb.med.umich.edu/ResPRE/ |
| TripletRes |
https://zhanglab.ccmb.med.umich.edu/TripletRes/ |
| RaptorX-Contact |
http://raptorx.uchicago.edu/ContactMap/ |
| MSA Transformer |
https://github.com/facebookresearch/esm |
| Deep Learning-Based Full-length Structure Prediction |
| AlphaFold |
https://github.com/deepmind/ |
| D-I-TASSER |
https://zhanglab.dcmb.med.umich.edu/D-I-TASSER/ |
| D-QUARK |
https://zhanglab.dcmb.med.umich.edu/D-QUARK/ |
| trRosetta |
https://yanglab.nankai.edu.cn/trRosetta/ |
| DMPfold |
Web server - http://bioinf.cs.ucl.ac.uk/psipred/
Downloadable version https://github.com/psipred/DMPfold
|
