Paper

Look mom, no experimental data! Learning to score protein-ligand interactions from simulations

Popov, Konstantin I, Tropsha, Alexander, Wellnitz, James, Brocidiacono, Michael

2025

Overview

Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In contrast, physics-based binding free energy calculations offer high accuracy across chemical space but are computationally prohibitive for large-scale screening. We propose a hybrid approach that approximates the accuracy of physics-based methods by training target-specific neural networks on molecular dynamics simulations of the protein in complex with random small molecules. Our method uses force matching to learn an implicit free energy landscape of ligand binding for each target. Evaluated on six proteins, our approach achieves competitive virtual screening performance using 100-500 \\(\\mu\\)s of MD simulations per target. Notably, this approach achieves state-of-the-art early enrichment when using the true pose for active compounds. These results highlight the potential of physics-informed learning for virtual screening on novel targets. We publicly release the code for this paper at https://github.com/molecularmodelinglab/lfm under the MIT license.

• Publisher: Cornell University Library, arXiv.org
• Subject: Binding / Deep learning / Free energy / Ligands / Machine learning / Molecular dynamics / Neural networks / Physics / Proteins / Screening / Simulation