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Updated: Feb 10, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
Published on: June 20, 2025
The future of molecular dynamics simulations in drug discovery
David W Borhani1, David E Shaw
1D. E. Shaw Research, New York, NY 10036, USA. David.Borhani@DEShawResearch.com
Abstract:
Molecular dynamics simulations can now track rapid processes--those occurring in less than about a millisecond--at atomic resolution for many biologically relevant systems. These simulations appear poised to exert a significant impact on how new drugs are found, perhaps even transforming the very process of drug discovery. We predict here future results we can expect from, and enhancements we need to make in, molecular dynamics simulations over the coming 25 years, and in so doing set out several Grand Challenges for the field. In the context of the problems now facing the pharmaceutical industry, we ask how we can best address drug discovery needs of the next quarter century using molecular dynamics simulations, and we suggest some possible approaches.
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