MLIPDiff: Guiding Denoising Diffusion Models for Structure-Based Drug Design via Machine-Learned Interatomic Potentials

arXiv:2610.33315v1 Announce Type: new Abstract: Diffusion models have become a dominant approach to structure-based drug design. However, because they are trained primarily to fit reference structures, they often place ligands in physically implausible poses that clash with the protein. We introduce MLIPDiff, an inference-time guidance method that can be applied to pretrained diffusion models for ligand generation. The method uses physics-informed guidance from UMA (Universal Models for Atoms), a machine-learned interatomic potential (MLIP). The guidance combines four weighted energy terms (protein-ligand interaction, ligand strain, steric clash, and pocket anchoring) and uses the original model checkpoint without retraining. On CrossDocked2020, MLIPDiff completely eliminates protein-ligand collisions while preserving the ligand's local geometry, improving bond-length distributions and physical plausibility relative to the base model. Compared to models such as NucleusDiff that are specifically designed to reduce atomic clashes, MLIPDiff achieves clash-free structures without compromising local geometry. It maintains the base model's PoseBusters pass rate and attains the best median Vina Score, Vina Min, and Vina Dock, surpassing both the base model and NucleusDiff, with a median of 59.6% of ligands per pocket binding more strongly than the reference. MLIPDiff thus addresses a limitation of prior methods by generating physically plausible structures with favorable predicted binding affinity using a single frozen model and no additional training.