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J Chem Inf Model. 2012 Jan 23;52(1):187-98. doi: 10.1021/ci200428t. Epub 2011 Dec 19.

Utilizing experimental data for reducing ensemble size in flexible-protein docking.

Author information

1
Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, USA.

Abstract

Efficient and sufficient incorporation of protein flexibility into docking is still a challenging task. Docking to an ensemble of protein structures has proven its utility for docking, but using a large ensemble of structures can reduce the efficiency of docking and can increase the number of false positives in virtual screening. In this paper, we describe the application of our new methodology, Limoc, to generate an ensemble of holo-like protein structures in combination with the relaxed complex scheme (RCS), to virtual screening. We describe different schemes to reduce the ensemble of protein structures to increase efficiency and enrichment quality. Utilizing experimental knowledge about actives for a target protein allows the reduction of ensemble members to a minimum of three protein structures, increasing enrichment quality and efficiency simultaneously.

PMID:
22146074
PMCID:
PMC3337782
DOI:
10.1021/ci200428t
[Indexed for MEDLINE]
Free PMC Article

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