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Nucleic Acids Res. 2012 Jul;40(Web Server issue):W471-7. doi: 10.1093/nar/gks372. Epub 2012 May 8.

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation.

Author information

1
Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA.

Abstract

We have developed a new COFACTOR webserver for automated structure-based protein function annotation. Starting from a structural model, given by either experimental determination or computational modeling, COFACTOR first identifies template proteins of similar folds and functional sites by threading the target structure through three representative template libraries that have known protein-ligand binding interactions, Enzyme Commission number or Gene Ontology terms. The biological function insights in these three aspects are then deduced from the functional templates, the confidence of which is evaluated by a scoring function that combines both global and local structural similarities. The algorithm has been extensively benchmarked by large-scale benchmarking tests and demonstrated significant advantages compared to traditional sequence-based methods. In the recent community-wide CASP9 experiment, COFACTOR was ranked as the best method for protein-ligand binding site predictions. The COFACTOR sever and the template libraries are freely available at http://zhanglab.ccmb.med.umich.edu/COFACTOR.

PMID:
22570420
PMCID:
PMC3394312
DOI:
10.1093/nar/gks372
[Indexed for MEDLINE]
Free PMC Article

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