Binding Mode Matters: Hotspot-Aware Drug Discovery via Explorative Preferences

arXiv:2611.14956v1 Announce Type: new Abstract: Discovering hit molecules requires not just high binding affinity, but also the identification of diverse binding modes, which are critical for experimental assays. Existing generative approaches have predominantly relied on optimizing a scalar docking score, obscuring the distinct contributions of key binding determinants. To this end, we introduce a paradigm shift by formulating target-based drug design as a multi-objective exploration task, where each objective explicitly corresponds to enhancing interactions with a specific hotspot. Here, we introduce BindMol, a novel generative framework driven by a customized multi-objective reinforcement learning algorithm.