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May 6, 2025Journal of Chemical Information and ModelingOpen Access

Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations

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Authors

SKS. Benjamin KobyEGEvgeny GutkinSPS. R. Patel

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Overview

Automated workflow improves resource allocation in binding simulations, suggesting cost-effective strategies.

Key Points

  • The aim is to optimize resource allocation for free energy simulations to enhance efficiency in drug discovery.
  • Developed an automated workflow for thermodynamic integration with on-the-fly resource optimization.
  • Used Jensen-Shannon distance for automatic equilibration detection and convergence testing.
  • Benchmarking conducted on cyclin-dependent kinase 2 and SARS-CoV-2 protease.
  • Achieved over 85% reduction in computational cost with comparable accuracy to traditional methods.
  • Demonstrated efficiency across various molecular transformations and binding scenarios.

Cite This Study

Koby et al. (2025) studied this question.

synapsesocial.com/papers/6a5b741e6b0a7c2cbcd2f88dhttps://doi.org/10.1021/acs.jcim.4c02107
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  4. 4Enhanced Sampling and Free Energy Calculations in Protein Simulations.2026 · 1 citations
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