Author:
Souza Paulo C. T.,Limongelli Vittorio,Wu Sangwook,Marrink Siewert J.,Monticelli Luca
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
Funder
European Research Council
Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
Agence Nationale de la Recherche
Subject
Biochemistry, Genetics and Molecular Biology (miscellaneous),Molecular Biology,Biochemistry
Cited by
25 articles.
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