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Title: Improvements, trends, and new ideas in molecular docking: 2012-2013 in review.
Austin Authors: Yuriev, Elizabeth;Holien, Jessica;Ramsland, Paul A 
Affiliation: School of Biomedical Sciences, CHIRI Biosciences, Curtin University, Perth, Western Australia, 6845, Australia
Centre for Biomedical Research, Burnet Institute, Melbourne, Victoria, 3004, Australia
Department of Surgery, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia
Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Victoria, 3004, Australia
Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
ACRF Rational Drug Discovery Centre and Structural Biology Laboratory, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia
Issue Date: Oct-2015 2015-03-21
Publication information: Journal of molecular recognition : JMR 2015; 28(10): 581-604
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.
DOI: 10.1002/jmr.2471
ORCID: 0000-0002-2107-2738
PubMed URL: 25808539
Type: Journal Article
Subjects: flexibility
fragment docking
machine learning
protein protein docking
receptor ensemble
virtual screening
Appears in Collections:Journal articles

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