Enhancing protein–ligand binding affinity predictions using neural network potentials

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Francesc Sabanés Zariquiey, Raimondas Galvelis, Emilio Gallicchio, John D. Chodera, Thomas E. Markland, Gianni De Fabritiis
Journal of Chemical Information and Modeling 64:1481, 2024.
[DOI] [preprint]

We show that hybrid neural network / molecular mechanics potentials can significantly improve accuracy over molecular mechanics potentials alone in predicting protein-ligand binding affinities.

End-to-end differentiable molecular mechanics force field construction

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Yuanqing Wang, Josh Fass, and John D. Chodera
Chemical Science 13:12016, 2022 [DOI] [arXiv] [pytorch code] [JAX code]

Molecular mechanics force fields have been a workhorse for computational chemistry and drug discovery. Here, we propose a new approach to force field parameterization in which graph convolutional networks are used to perceive chemical environments and assign molecular mechanics (MM) force field parameters. The entire process of chemical perception and parameter assignment is differentiable end-to-end with respect to model parameters, allowing new force fields to be easily constructed from MM or QM force fields, extended, and applied to arbitrary biomolecules.

Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials

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Dominic A. Rufa, Hannah E. Bruce Macdonald, Josh Fass, Marcus Wieder, Patrick B. Grinaway, Adrian E. Roitberg, Olexandr Isayev, and John D. Chodera.
Preprint ahead of submission.
[bioRxiv] [GitHub]

In this first use of hybrid machine learning / molecular mechanics (ML/MM) potentials for alchemical free energy calculations, we demonstrate how the improved modeling of intramolecular ligand energetics offered by the quantum machine learning potential ANI-2x can significantly improve the accuracy in predicting kinase inhibitor binding free energy by reducing the error from 0.97~kcal/mol to 0.47~kcal/mol, which could drastically reduce the number of compounds that must be synthesized in lead optimization campaigns for minimal additional computational cost.