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Molecular docking as a popular tool in drug design, an in silico travel

Authors de Ruyck J, Brysbaert G, Blossey R, Lensink M

Received 29 January 2016

Accepted for publication 12 March 2016

Published 24 June 2016 Volume 2016:9 Pages 1—11


Checked for plagiarism Yes

Review by Single anonymous peer review

Peer reviewer comments 2

Editor who approved publication: Dr Juan Fernandez-Recio

Jerome de Ruyck, Guillaume Brysbaert, Ralf Blossey, Marc F Lensink

University Lille, CNRS UMR8576 UGSF, Lille, France

Abstract: New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism- or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein–protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.

Keywords: structure-based drug design, protein–protein docking, quaternary structure prediction, residue interaction networks, RINs, water position

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