Ensemble Docking in Drug Discovery

Rommie E Amaro; Jerome Baudry; John Chodera; Özlem Demir; J Andrew McCammon; Yinglong Miao; Jeremy C Smith

doi:10.1016/j.bpj.2018.02.038

Ensemble Docking in Drug Discovery

Biophys J. 2018 May 22;114(10):2271-2278. doi: 10.1016/j.bpj.2018.02.038. Epub 2018 Mar 30.

Authors

Rommie E Amaro¹, Jerome Baudry², John Chodera³, Özlem Demir¹, J Andrew McCammon¹, Yinglong Miao⁴, Jeremy C Smith⁵

Affiliations

¹ Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
² University of Alabama at Huntsville, Huntsville, Alabama.
³ University of California, Berkeley, Berkeley, California.
⁴ Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, Kansas.
⁵ UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee. Electronic address: smithjc@ornl.gov.

Abstract

Ensemble docking corresponds to the generation of an "ensemble" of drug target conformations in computational structure-based drug discovery, often obtained by using molecular dynamics simulation, that is used in docking candidate ligands. This approach is now well established in the field of early-stage drug discovery. This review gives a historical account of the development of ensemble docking and discusses some pertinent methodological advances in conformational sampling.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Review

MeSH terms

Drug Discovery / methods*
Kinetics
Molecular Docking Simulation*
Protein Conformation
Software

Abstract

Publication types

MeSH terms

Grants and funding