ArticleCommunications chemistry2024
Accurate protein-ligand binding free energy estimation using QM/MM on multi-conformers predicted from classical mining minima.
Article in Communications chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
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- Construction of a multi-label odor prediction model based on molecular structures and olfactory receptor binding profiles with a novel interpretability framework.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2026Article
- Stereoselective synthesis of 1'-α-cyano carbocyclic pyrimidine nucleoside analogsOrganic & biomolecular chemistry · 2026Article
- Efficient and accurate spatial mixing of machine learned interatomic potentials for materials science.npj computational materials · 2026Article
- Perspectives on Hybridizing Quantum Mechanics and Artificial Intelligence for Drug Design.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Article
- Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface.Journal of chemical information and modeling · 2025Article
- Fragment-based drug discovery: A graphical review.Current research in pharmacology and drug discovery · 2025Review
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Authors and funding
2 authors.
Funding
Abstract
Accurate prediction of binding free energy is crucial for the rational design of drug candidates and understanding protein-ligand interactions. To address this, we have developed four protocols that combine QM/MM calculations and the mining minima (M2) method, tested on 9 targets and 203 ligands. Our protocols carry out free energy processing with or without conformational search on the selected conformers obtained from M2 calculations, where their force field atomic charge parameters are substituted with those obtained from a QM/MM calculation. The method achieved a high Pearson's correlation coefficient (0.81) with experimental binding free energies across diverse targets, demonstrating its generality. Using a differential evolution algorithm with a universal scaling factor of 0.2, we achieved a low mean absolute error of 0.60 kcal mol
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