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Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
Author(s) -
Yuriev Elizabeth,
Holien Jessica,
Ramsland Paul A.
Publication year - 2015
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.2471
Subject(s) - docking (animal) , virtual screening , computer science , solvation , computational biology , artificial intelligence , machine learning , chemistry , molecular dynamics , computational chemistry , biology , molecule , medicine , nursing , organic chemistry
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.