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Nucleic Acids Res. 2013 Jul;41(Web Server issue):W384-8. doi: 10.1093/nar/gkt458. Epub 2013 Jun 3.

GalaxyRefine: Protein structure refinement driven by side-chain repacking.

Author information

1
Department of Chemistry, Seoul National University, Seoul 151-747, Korea.

Abstract

The quality of model structures generated by contemporary protein structure prediction methods strongly depends on the degree of similarity between the target and available template structures. Therefore, the importance of improving template-based model structures beyond the accuracy available from template information has been emphasized in the structure prediction community. The GalaxyRefine web server, freely available at http://galaxy.seoklab.org/refine, is based on a refinement method that has been successfully tested in CASP10. The method first rebuilds side chains and performs side-chain repacking and subsequent overall structure relaxation by molecular dynamics simulation. According to the CASP10 assessment, this method showed the best performance in improving the local structure quality. The method can improve both global and local structure quality on average, when used for refining the models generated by state-of-the-art protein structure prediction servers.

PMID:
23737448
PMCID:
PMC3692086
DOI:
10.1093/nar/gkt458
[Indexed for MEDLINE]
Free PMC Article

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