GalaxyRefine: protein structure refinement driven by side-chain repacking

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ID: 296455
2013
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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.
Reference Key
openalex_W1998917415 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Lim Heo, Hahnbeom Park, Chaok Seok
Journal Nucleic Acids Research
Year 2013
DOI
10.1093/nar/gkt458
URL
https://doi.org/10.1093/nar/gkt458
Keywords Keywords not found

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