FlowPacker: protein side-chain packing with torsional flow matching.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 39786861.
- Also identified by DOI 10.1093/bioinformatics/btaf010 and PMC identifier 11886813.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design. 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. Code is available at https://gitlab.com/mjslee0921/flowpacker.
Medical subject headings
- Proteins
- Software