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Int. J. Mol. Sci. 2010, 11(8), 3016-3034; doi:10.3390/ijms11083016
Review

Advances and Challenges in Protein-Ligand Docking

1,2,3,4
 and
1,2,3,4,*
1 Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO 65211, USA 2 Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA 3 Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA 4 Informatics Institute, University of Missouri, Columbia, MO 65211, USA
* Author to whom correspondence should be addressed.
Received: 11 May 2010 / Revised: 30 July 2010 / Accepted: 4 August 2010 / Published: 18 August 2010
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Abstract

Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the recent advances of protein flexibility, ligand sampling, and scoring functions—the three important aspects in protein-ligand docking. Challenges and possible future directions are discussed in the Conclusion.
Keywords: protein flexibility; ligand sampling; scoring functions; molecular docking; protein-ligand interactions protein flexibility; ligand sampling; scoring functions; molecular docking; protein-ligand interactions
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).
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Huang, S.-Y.; Zou, X. Advances and Challenges in Protein-Ligand Docking. Int. J. Mol. Sci. 2010, 11, 3016-3034.

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