Narrowing the gap between machine learning scoring functions and free energy perturbation using augmented data

Journal article

Machine learning offers great promise for fast and accurate binding affinity predictions. However, current models lack robust evaluation and fail on tasks encountered in (hit-to-) lead optimisation, such as ranking the binding affinity of a congeneric series of ligands, thereby limiting their application in drug discovery. Here, we address these issues by first introducing a novel attention-based graph neural network model called AEV-PLIG (atomic environment vector–protein ligand interaction graph). Second, we introduce a new and more realistic out-of-distribution test set called the OOD Test. We benchmark our model on this set, CASF-2016, and a test set used for free energy perturbation (FEP) calculations, that not only highlights the competitive performance of AEV-PLIG, but provides a realistic assessment of machine learning models with rigorous physics-based approaches. Moreover, we demonstrate how leveraging augmented data (generated using template-based modelling or molecular docking) can significantly improve binding affinity prediction correlation and ranking on the FEP benchmark (weighted mean PCC and Kendall’s τ increases from 0.41 and 0.26 to 0.59 and 0.42). These strategies together are closing the performance gap with FEP calculations (FEP+ achieves weighted mean PCC and Kendall’s τ of 0.68 and 0.49 on the FEP benchmark) while being ~400,000 times faster.

Authors: Valsson, Í; Warren, MT; Deane, CM; Magarkar, A; Morris, GM

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Communications Chemistry
• Volume: 8
• Issue: 1
• Article number: 41
• Publication date: 2025-02-08
• Acceptance date: 2025-01-23
• DOI: 10.1038/s42004-025-01428-y
• EISSN: 2399-3669
• Language: English