Key Topics in Molecular Docking for Drug Design

Pedro H. M. Torres; Ana C. R. Sodero; Paula Jofily; Floriano P. Silva-Jr

doi:10.3390/ijms20184574

journal article Open Access Sep 15, 2019

Key Topics in Molecular Docking for Drug Design

Pedro H. M. Torres

Ana C. R. Sodero Paula Jofily

Floriano P. Silva-Jr

International Journal of Molecular Sciences Vol. 20 No. 18 pp. 4574 · MDPI AG

View at Publisher Save 10.3390/ijms20184574

Abstract

Molecular docking has been widely employed as a fast and inexpensive technique in the past decades, both in academic and industrial settings. Although this discipline has now had enough time to consolidate, many aspects remain challenging and there is still not a straightforward and accurate route to readily pinpoint true ligands among a set of molecules, nor to identify with precision the correct ligand conformation within the binding pocket of a given target molecule. Nevertheless, new approaches continue to be developed and the volume of published works grows at a rapid pace. In this review, we present an overview of the method and attempt to summarise recent developments regarding four main aspects of molecular docking approaches: (i) the available benchmarking sets, highlighting their advantages and caveats, (ii) the advances in consensus methods, (iii) recent algorithms and applications using fragment-based approaches, and (iv) the use of machine learning algorithms in molecular docking. These recent developments incrementally contribute to an increase in accuracy and are expected, given time, and together with advances in computing power and hardware capability, to eventually accomplish the full potential of this area.

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References

Details

Published: Sep 15, 2019
Vol/Issue: 20(18)
Pages: 4574
License: View

Authors

P

Pedro H. M. Torres

Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK

A

Ana C. R. Sodero

Department of Drugs and Medicines; School of Pharmacy; Federal University of Rio de Janeiro, Rio de Janeiro 21949-900, RJ, Brazil

P

Paula Jofily

Laboratório de Modelagem e Dinâmica Molecular, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21949-900, RJ, Brazil

F

Floriano P. Silva-Jr

Laboratório de Bioquímica Experimental e Computacional de Fármacos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro 21949-900, RJ, Brazil

Funding

Conselho Nacional de Desenvolvimento Cientifico e Tecnologico Award: 304059/2018-8

Academy of Medical Sciences Award: ITPMZO55

Cite This Article

Pedro H. M. Torres, Ana C. R. Sodero, Paula Jofily, et al. (2019). Key Topics in Molecular Docking for Drug Design. International Journal of Molecular Sciences, 20(18), 4574. https://doi.org/10.3390/ijms20184574

Key Topics in Molecular Docking for Drug Design

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