Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design

arXiv:2310.05764v3 Announce Type: replace
Abstract: A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy storage. Towards this goal, we first develop HarmonicFlow, an improved generative process over 3D protein-ligand binding structures based on our self-conditioned flow matching objective. FlowSite extends this flow model to jointly generate a protein pocket's discrete residue types and the molecule's binding 3D structure. …

abstract applications arxiv cs.ai cs.lg design designing energy energy storage flow function generative molecules process protein small storage synthesis type