title: Are predicted protein structures of any value for binding site prediction and virtual ligand screening?
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.
authors: 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
authors: Jeffrey
authors: J
authors: Skolnick
authors: Hongyi
authors: H
authors: Zhou
authors: Mu
authors: M
authors: Gao
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D055808:Drug Discovery; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008024:Ligands; D011506:Proteins