ArticleThe journal of physical chemistry letters2024
Absolute Binding Free Energies with OneOPES.
Article in The journal of physical chemistry letters, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Methods for the establishment of enzymatic mechanisms - from QM to ML.Chemical science · 2026Review
- Deciphering the evolutionary origin of the enantioselectivity of short-chain dehydrogenases from plants toward 1-borneol.Nature communications · 2026Article
- Molecular Dynamics Workflows to Compute Large-Scale Sets of Absolute Binding Free Energies Aiding Drug Candidate and Binding Pose Selection.Journal of chemical theory and computation · 2026Article
- A Transferable and Robust Computational Framework for Class A GPCR Activation Free Energies.The journal of physical chemistry letters · 2026Article
- Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization.The journal of physical chemistry. B · 2026Article
- Quantum mechanics in drug design: Progress, challenges, and future frontiers.Communicative & integrative biology · 2026Review
- 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
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.Journal of chemical information and modeling · 2024Article
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Authors and funding
6 authors.
Funding
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Abstract
The calculation of absolute binding free energies (ABFEs) for protein-ligand systems has long been a challenge. Recently, refined force fields and algorithms have improved the quality of the ABFE calculations. However, achieving the level of accuracy required to inform drug discovery efforts remains difficult. Here, we present a transferable enhanced sampling strategy to accurately calculate absolute binding free energies using OneOPES with simple geometric collective variables. We tested the strategy on two protein targets, BRD4 and Hsp90, complexed with a total of 17 chemically diverse ligands, including both molecular fragments and drug-like molecules. Our results show that OneOPES accurately predicts protein-ligand binding affinities with a mean unsigned error within 1 kcal mol
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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 Socratic graph.