Table 5.8.1.
Frequently Used Resources for Protein Structure Prediction
| Name and URL | Note |
|---|---|
| I-TASSER http://zhanglab.ccmb.med.umich.edu/I-TASSER |
Hierarchal structure prediction by reassembling threading fragments based on replica-exchange Monte Carlo simulation (Yang and Zhang, 2015) |
| Rosetta http://robetta.bakerlab.org |
Ab initio structure prediction by assembling 3- and 9-mer fragments based on simulated annealing Monte Carlo simulation (Kim et al., 2004) |
| QUARK http://zhanglab.ccmb.med.umich.edu/QUARK |
Ab initio structure folding by assembling continuously distributed fragments based on replica-exchange Monte Carlo simulations (Xu and Zhang, 2012) |
| HHpred http://toolkit.tuebingen.mpg.de/hhpred |
Threading template identification based on hidden Markov model alignments (Soding et al., 2005) |
| Phyre2 http://www.sbg.bio.ic.ac.uk/phyre2 |
Threading template identification using profile-profile alignments (recent update uses HHpred) (Kelley et al., 2015) |
| GenThreader http://bioinf.cs.ucl.ac.uk/psipred |
Threading template identification based on profile-profile comparison (Buchan et al., 2010) |
| RaptorX http://raptorx.uchicago.edu |
Threading template identification using nonlinear alignment scores (Källberg et al., 2012) |
| FFAS http://ffas.burnham.org |
Threading template recognition by profile-profile alignment (Jaroszewski et al., 2005) |
| TASSER http://cssb.biology.gatech.edu/skolnick/webservice/TASSER/index.html |
Structure assembly from threading fragments based on Monte Carlo simulation (Zhang and Skolnick, 2004a; Zhou and Skolnick, 2007) |
| LOMETS http://zhanglab.ccmb.med.umich.edu/LOMETS |
Meta-threading server to identify structural templates using multiple threading programs (Wu and Zhang, 2007) |
| Modeller https://salilab.org/modeller |
Package for comparative structure modeling by satisfying spatial restraints (Sali and Blundell, 1993) |
| Swiss-Model http://swissmodel.expasy.org |
Homologous modeling server using templates from Blast and HHpred (Biasini et al., 2014) |
| CASP http://predictioncenter.org |
Platform for community-wide benchmark of protein structure prediction (Moult et al., 2014) |
| CAMEO http://cameo3d.org |
Platform for continuous evaluation of structure and function prediction methods (Haas et al., 2013) |