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Nucleic Acids Res. 2011 Jul;39(Web Server issue):W210-4. doi: 10.1093/nar/gkr352. Epub 2011 May 16.

The FALC-Loop web server for protein loop modeling.

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

Abstract

The FALC-Loop web server provides an online interface for protein loop modeling by employing an ab initio loop modeling method called FALC (fragment assembly and analytical loop closure). The server may be used to construct loop regions in homology modeling, to refine unreliable loop regions in experimental structures or to model segments of designed sequences. The FALC method is computationally less expensive than typical ab initio methods because the conformational search space is effectively reduced by the use of fragments derived from a structure database. The analytical loop closure algorithm allows efficient search for loop conformations that fit into the protein framework starting from the fragment-assembled structures. The FALC method shows prediction accuracy comparable to other state-of-the-art loop modeling methods. Top-ranked model structures can be visualized on the web server, and an ensemble of loop structures can be downloaded for further analysis. The web server can be freely accessed at http://falc-loop.seoklab.org/.

PMID:
21576220
PMCID:
PMC3125760
DOI:
10.1093/nar/gkr352
[Indexed for MEDLINE]
Free PMC Article
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