Improvements,trends, and new ideas in molecular docking: 2012–2013 in review |
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| Authors: | Elizabeth Yuriev Jessica Holien Paul A Ramsland |
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| Institution: | 1. Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia;2. ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia;3. Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, Australia;4. Department of Surgery Austin Health, University of Melbourne, Melbourne, Victoria, Australia;5. Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, Australia;6. School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, Australia |
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| Abstract: | Molecular docking is a computational method for predicting the placement of ligands in the binding sites of their receptor(s). In this review, we discuss the methodological developments that occurred in the docking field in 2012 and 2013, with a particular focus on the more difficult aspects of this computational discipline. The main challenges and therefore focal points for developments in docking, covered in this review, are receptor flexibility, solvation, scoring, and virtual screening. We specifically deal with such aspects of molecular docking and its applications as selection criteria for constructing receptor ensembles, target dependence of scoring functions, integration of higher‐level theory into scoring, implicit and explicit handling of solvation in the binding process, and comparison and evaluation of docking and scoring methods. Copyright © 2015 John Wiley & Sons, Ltd. |
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| Keywords: | flexibility fragment docking machine learning protein protein docking receptor ensemble scoring solvation virtual screening |
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