FlowPacker: protein side-chain packing with torsional flow matching

Abstract

Motivation: Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein–protein interactions and facilitate de novo protein design. Results: Here, we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime. We further show that FlowPacker can be used to inpaint missing side-chain coordinates and also for multimeric targets, and exhibits strong performance on a test set of antibody–antigen complexes.