Evaluating docking programs: keeping the playing field level

Journal of Computer-aided Molecular Design
John W Liebeschuetz

Abstract

Over recent years many enrichment studies have been published which purport to rigorously compare the performance of two or more docking protocols. It has become clear however that such studies often have flaws within their methodologies, which cast doubt on the rigour of the conclusions. Setting up such comparisons is fraught with difficulties and no best mode of practice is available to guide the experimenter. Careful choice of structural models and ligands appropriate to those models is important. The protein structure should be representative for the target. In addition the set of active ligands selected should be appropriate to the structure in cases where different forms of the protein bind different classes of ligand. Binding site definition is also an area in which errors arise. Particular care is needed in deciding which crystallographic waters to retain and again this may be predicated by knowledge of the likely binding modes of the ligands making up the active ligand list. Geometric integrity of the ligand structures used is clearly important yet it is apparent that published sets of actives + decoys may contain sometimes high proportions of incorrect structures. Choice of protocol for docking and analysis needs care...Continue Reading

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Citations

Mar 14, 2008·Journal of Computer-aided Molecular Design·Ajay N Jain, Anthony Nicholls
Sep 17, 2011·Bioorganic & Medicinal Chemistry·Adel HamzaChang-Guo Zhan
Feb 15, 2011·Bioorganic & Medicinal Chemistry·Ralf HeinkeWolfgang Sippl
Apr 28, 2009·Journal of Molecular Graphics & Modelling·Sara A Moura-TamamesPedro A Fernandes
Oct 28, 2019·Journal of Computer-aided Molecular Design·Ann E ClevesAjay N Jain
May 30, 2009·Journal of Chemical Information and Modeling·Jason B CrossChristine Humblet
May 13, 2009·Journal of Chemical Information and Modeling·Sebastian G Rohrer, Knut Baumann
Mar 23, 2011·Journal of Chemical Information and Modeling·Jesús M PlanesasVioleta I Pérez-Nueno
Jun 6, 2013·Journal of Chemical Information and Modeling·Jacob D DurrantJ Andrew McCammon
Apr 10, 2020·Journal of Chemical Information and Modeling·Ann E Cleves, Ajay N Jain

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