Ensemble Docking in Drug Discovery
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Updated: Feb 12, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
Rommie E Amaro1, Jerome Baudry2, John Chodera3
1Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California.
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.
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