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Updated: Aug 14, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
The role and application of in silico docking in chemical genomics research
Aldo Jongejan1, Chris de Graaf, Nico P E Vermeulen
1Division of Medicinal Chemistry, Leiden/Amsterdam Center for Drug Research, Faculty of Sciences, Vrije Universiteit, Amsterdam, The Netherlands.
Abstract:
In silico docking techniques are being used to investigate the complementarity at the molecular level of a ligand and a protein target. As such, docking studies can be used to identify the structural features that are important for binding and for in silico screening efforts in which suitable binding partners can be identified. Here we describe a practical approach for setting up docking simulations using different docking programs. We also cover the analysis and rescoring of the obtained docking poses. Possible pitfalls in the docking studies are discussed and hints are provided to resolve commonly occurring problems.
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