{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T22:28:13Z","timestamp":1780957693711,"version":"3.54.1"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,1,9]],"date-time":"2025-01-09T00:00:00Z","timestamp":1736380800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","award":["PJT-166008"],"award-info":[{"award-number":["PJT-166008"]}],"id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein\u2013protein interactions and facilitate de novo protein design.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>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\u2013antigen complexes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Code is available at https:\/\/gitlab.com\/mjslee0921\/flowpacker.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf010","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T15:20:40Z","timestamp":1736263240000},"source":"Crossref","is-referenced-by-count":9,"title":["FlowPacker: protein side-chain packing with torsional flow matching"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6410-2706","authenticated-orcid":false,"given":"Jin Sub","family":"Lee","sequence":"first","affiliation":[{"name":"Department of Molecular Genetics, University of Toronto , Toronto, Ontario, M5S 3K3,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip M","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics, University of Toronto , Toronto, Ontario, M5S 3K3,","place":["Canada"]},{"name":"Department of Computer Science, University of Toronto , Toronto, Ontario, M5S 2E4,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,1,9]]},"reference":[{"key":"2025030711571789200_btaf010-B1","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/s41586-024-07487-w","article-title":"Accurate structure prediction of biomolecular interactions with AlphaFold 3","volume":"630","author":"Abramson","year":"2024","journal-title":"Nature"},{"key":"2025030711571789200_btaf010-B2","doi-asserted-by":"crossref","first-page":"3031","DOI":"10.1021\/acs.jctc.7b00125","article-title":"The Rosetta all-atom energy function for macromolecular modeling and design","volume":"13","author":"Alford","year":"2017","journal-title":"J Chem Theory Comput"},{"key":"2025030711571789200_btaf010-B3","author":"Chen","year":"2024"},{"key":"2025030711571789200_btaf010-B4","author":"Chen","year":"2018"},{"key":"2025030711571789200_btaf010-B5","first-page":"16344","article-title":"Flashattention: fast and memoryefficient exact attention with io-awareness","volume":"35","author":"Dao","year":"2022","journal-title":"Adv Neural Inf Process Syst"},{"key":"2025030711571789200_btaf010-B6","doi-asserted-by":"crossref","first-page":"D1140","DOI":"10.1093\/nar\/gkt1043","article-title":"SAbDab: the structural antibody 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