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Review
. 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?

Jeffrey Skolnick  1 , Hongyi Zhou, Mu Gao
Affiliations
Review

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

Jeffrey Skolnick et al. Curr Opin Struct Biol. 2013 Apr.

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.

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Figures

Figure 1
Figure 1
Flowchart of Ligand Homology Modeling (LHM). Target and template proteins are colored in blue and green, respectively, and ligands are colored in purple.
See this image and copyright information in PMC

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