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Molecules 2014, 19(7), 10150-10176; doi:10.3390/molecules190710150
Review

Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design

1,2
 and 1,2,3,4,*
1 Informatics Institute, University of Missouri, Columbia, MO 65211, USA 2 Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA 3 Department of Physics & Astronomy, University of Missouri, Columbia, MO 65211, USA 4 Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
* Author to whom correspondence should be addressed.
Received: 23 April 2014 / Revised: 13 June 2014 / Accepted: 2 July 2014 / Published: 11 July 2014
(This article belongs to the Special Issue In-Silico Drug Design and In-Silico Screening)
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Abstract

The docking methods used in structure-based virtual database screening offer the ability to quickly and cheaply estimate the affinity and binding mode of a ligand for the protein receptor of interest, such as a drug target. These methods can be used to enrich a database of compounds, so that more compounds that are subsequently experimentally tested are found to be pharmaceutically interesting. In addition, like all virtual screening methods used for drug design, structure-based virtual screening can focus on curated libraries of synthesizable compounds, helping to reduce the expense of subsequent experimental verification. In this review, we introduce the protein-ligand docking methods used for structure-based drug design and other biological applications. We discuss the fundamental challenges facing these methods and some of the current methodological topics of interest. We also discuss the main approaches for applying protein-ligand docking methods. We end with a discussion of the challenging aspects of evaluating or benchmarking the accuracy of docking methods for their improvement, and discuss future directions.
Keywords: protein-ligand interactions; structure-based drug design; molecular docking protein-ligand interactions; structure-based drug design; molecular docking
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Grinter, S.Z.; Zou, X. Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design. Molecules 2014, 19, 10150-10176.

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