ArticleJournal of chemical information and modeling2022
Accurate Binding Free Energy Method from End-State MD Simulations.
Article in Journal of chemical information and modeling, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- Structure based drug design and machine learning approaches for identifying natural inhibitors against the human αβIII tubulin isotype.Scientific reports · 2025Article
- A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations.Journal of chemical information and modeling · 2025Article
- Substituents introduction of methyl and methoxy functional groups on resveratrol stabilizes mTOR binding for autophagic cell death induction.Scientific reports · 2025Article
- From Apo to Ligand-Bound: Unraveling PPARγ-LBD Conformational Shifts via Advanced Molecular Dynamics.ACS omega · 2025Article
- DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.Journal of chemical information and modeling · 2025Article
- Structural bioinformatics for rational drug design.Research and practice in thrombosis and haemostasis · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Insights and Challenges in Correcting Force Field Based Solvation Free Energies Using a Neural Network Potential.The journal of physical chemistry. B · 2024Article
- Molecular Recognition between Carbon Dioxide and Biodegradable Hydrogel Models: A Density Functional Theory (DFT) Investigation.Gels (Basel, Switzerland) · 2024Article
- Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 MJournal of computer-aided molecular design · 2024Article
- Phanto-IDP: compact model for precise intrinsically disordered protein backbone generation and enhanced sampling.Briefings in bioinformatics · 2023Article
- Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.The journal of physical chemistry. B · 2023Article
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Authors and funding
4 authors.
Funding
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Abstract
Herein, we introduce a new strategy to estimate binding free energies using end-state molecular dynamics simulation trajectories. The method is adopted from linear interaction energy (LIE) and ANI-2x neural network potentials (machine learning) for the atomic simulation environment (ASE). It predicts the single-point interaction energies between ligand-protein and ligand-solvent pairs at the accuracy of the wb97x/6-31G* level for the conformational space that is sampled by molecular dynamics (MD) simulations. Our results on 54 protein-ligand complexes show that the method can be accurate and have a correlation of
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