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Curr Opin Struct Biol. 2013 Apr;23(2):191-7. doi: 10.1016/j.sbi.2013.01.009. Epub 2013 Feb 14.

Are predicted protein structures of any value for binding site prediction and virtual ligand screening?

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1
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA. skolnick@gatech.edu

Abstract

The recently developed field of ligand homology modeling (LHM) that extends the ideas of protein homology modeling to the prediction of ligand binding sites and for use in virtual ligand screening has emerged as a powerful new approach. Unlike traditional docking methodologies, LHM can be applied to low-to-moderate resolution predicted as well as experimental structures with little if any diminution in performance; thereby enabling ≈ 75% of an average proteome to have potentially significant virtual screening predictions. In large scale benchmarking, LHM is able to predict off-target ligand binding. Thus, despite the widespread belief to the contrary, low-to-moderate resolution predicted structures have considerable utility for biochemical function prediction.

PMID:
23415854
PMCID:
PMC3659186
DOI:
10.1016/j.sbi.2013.01.009
[Indexed for MEDLINE]
Free PMC Article
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