ArticleJournal of chemical theory and computation2024
Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Free energy calculations in molecular modeling: from classical methods to machine learning.Journal of molecular modeling · 2026Review
- A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies.The journal of physical chemistry letters · 2026Article
- The Arch from the Stones: Understanding Protein Folding Energy Landscapes via Bioinspired Collective Variables.The journal of physical chemistry letters · 2025Article
- Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation.Journal of chemical theory and computation · 2025Article
- PLUMED Tutorials: A collaborative, community-driven learning ecosystem.The Journal of chemical physics · 2025Article
- Nonequilibrium Binding Free Energy Simulations: Minimizing Dissipation.Journal of chemical theory and computation · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Estimating absolute binding free energies from molecular simulations is a key step in computer-aided drug design pipelines, but the agreement between computational results and experiments is still very inconsistent. Both the accuracy of the computational model and the quality of the statistical sampling contribute to this discrepancy, yet disentangling the two remains a challenge. In this study, we present an automated protocol based on OneOPES, an enhanced sampling method that exploits replica exchange and can accelerate several collective variables to address the sampling problem. We apply this protocol to 37 host-guest systems. The simplicity of setting up the simulations and producing well-converged binding free energy estimates without the need to optimize simulation parameters provides a reliable solution to the sampling problem. This, in turn, allows for a systematic force field comparison and ranking according to the correlation between simulations and experiments, which can inform the selection of an appropriate model. The protocol can be readily adapted to test more force field combinations and study more complex protein-ligand systems, where the choice of an appropriate physical model is often based on heuristic considerations rather than systematic optimization.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.