ArticleThe journal of physical chemistry. B2023
Revisiting MMPBSA by Adoption of MC-Based Surface Area/Volume, ANI-ML Potentials, and Two-Valued Interior Dielectric Constant.
Article in The journal of physical chemistry. B, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Virtual Screening of Bacteriocins From Lactic Acid Bacteria Against Monkeypox DNA Polymerase: Sakacin P and Mundticin KS Emerge as Promising Candidates.Food science & nutrition · 2026Article
- Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.The journal of physical chemistry. B · 2025Article
- DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.Journal of chemical information and modeling · 2025Article
- Article
- Benchmarking ANI potentials as a rescoring function and screening FDA drugs for SARS-CoV-2 MJournal of computer-aided molecular design · 2024Article
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Authors and funding
4 authors.
Funding
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Abstract
Here, we report the accuracy improvements of molecular mechanics Poisson-Boltzmann surface area (MMPBSA) calculations by adoption of ANI-ML potentials in replacement of MM terms, the use of solvent-accessible surface area (SASA) and volume (SAV) values from the Monte Carlo sampling of the probe, and introducing two different interior dielectric constants for electrostatic interactions of protein-ligand (P-L) and polar solvation term in the MMPBSA calculations. Our results show that the Pearson correlation coefficients of MMPBSA-calculated values with respect to experimental binding free energies can be drastically improved from 0.48 to 0.90 by adoption of ANI-ML potentials in replacement of MM energy terms in the equation, referred to as ANI-PBSA. Moreover, we show that the SASA/SAV-combined equation in the scaled particle theory (SPT) can be a better choice to model nonpolar solvation term, reaching nearly the same accuracy by ANI-PBSA calculations. Finally, we introduce two different values of interior dielectric constants, which could be an alternative strategy between the single and variable constant definitions.
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Registered trials
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