{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T01:57:36Z","timestamp":1776304656010,"version":"3.50.1"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T00:00:00Z","timestamp":1688515200000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2021-03979"],"award-info":[{"award-number":["2021-03979"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004063","name":"Knut and Alice Wallenberg Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Despite near-experimental accuracy on single-chain predictions, there is still scope for improvement among multimeric predictions. Methods like AlphaFold-Multimer and FoldDock can accurately model dimers. However, how well these methods fare on larger complexes is still unclear. Further, evaluation methods of the quality of multimeric complexes are not well established.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We analysed the performance of AlphaFold-Multimer on a homology-reduced dataset of homo- and heteromeric protein complexes. We highlight the differences between the pairwise and multi-interface evaluation of chains within a multimer. We describe why certain complexes perform well on one metric (e.g. TM-score) but poorly on another (e.g. DockQ). We propose a new score, Predicted DockQ version 2 (pDockQ2), to estimate the quality of each interface in a multimer. Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>All scripts, models, and data used to perform the analysis in this study are freely available at https:\/\/gitlab.com\/ElofssonLab\/afm-benchmark.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad424","type":"journal-article","created":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T15:27:29Z","timestamp":1688570849000},"source":"Crossref","is-referenced-by-count":159,"title":["Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes"],"prefix":"10.1093","volume":"39","author":[{"given":"Wensi","family":"Zhu","sequence":"first","affiliation":[{"name":"Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University , Solna 171 21, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7748-2501","authenticated-orcid":false,"given":"Aditi","family":"Shenoy","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University , Solna 171 21, Sweden"}]},{"given":"Petras","family":"Kundrotas","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University , Solna 171 21, Sweden"},{"name":"Center for Computational Biology, The University of Kansas , Lawrence, KS 66047, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7115-9751","authenticated-orcid":false,"given":"Arne","family":"Elofsson","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory and Department of Biochemistry and Biophysics, Stockholm University , Solna 171 21, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2023,7,5]]},"reference":[{"key":"2023071423264613600_btad424-B1","doi-asserted-by":"crossref","first-page":"e0161879","DOI":"10.1371\/journal.pone.0161879","article-title":"DockQ: a quality measure for protein\u2013protein docking models","volume":"11","author":"Basu","year":"2016","journal-title":"PLoS One"},{"key":"2023071423264613600_btad424-B151","doi-asserted-by":"crossref","first-page":"4932","DOI":"10.1038\/s41598-017-05084-8","article-title":"Functional determinants of protein assembly into homomeric complexes","volume":"7","author":"Bergendahl","year":"2017","journal-title":"Sci Rep"},{"key":"2023071423264613600_btad424-B2","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1038\/s41467-022-28865-w","article-title":"Improved prediction of protein\u2013protein interactions using AlphaFold2","volume":"13","author":"Bryant","year":"2022","journal-title":"Nat Commun"},{"key":"2023071423264613600_btad424-B152","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1146\/annurev.biophys.37.092707.153558","article-title":"The protein folding problem","volume":"37","author":"Dill","year":"2008","journal-title":"Annu Rev Biophys"},{"key":"2023071423264613600_btad424-B153","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein-protein docking approach based on biochemical or biophysical information","volume":"125","author":"Dominguez","year":"2003","journal-title":"J Am Chem Soc"},{"key":"2023071423264613600_btad424-B154","doi-asserted-by":"crossref","first-page":"1818","DOI":"10.1002\/prot.24079","article-title":"Multi-LZerD: multiple protein docking for asymmetric complexes","volume":"80","author":"Esquivel-Rodr\u00edguez","year":"2012","journal-title":"Proteins"},{"key":"2023071423264613600_btad424-B3","author":"Evans","year":"2022"},{"key":"2023071423264613600_btad424-B155","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1038\/s41467-022-29394-2","article-title":"AF2Complex predicts direct physical interactions in multimeric proteins with deep learning","volume":"13","author":"Gao","year":"2022","journal-title":"Nat Commun"},{"key":"2023071423264613600_btad424-B4","doi-asserted-by":"crossref","first-page":"D559","DOI":"10.1093\/nar\/gky973","article-title":"CORUM: the comprehensive resource of mammalian protein complexes\u20142019","volume":"47","author":"Giurgiu","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023071423264613600_btad424-B5","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/S0020-0190(00)00142-3","article-title":"A clustering algorithm based on graph connectivity","volume":"76","author":"Hartuv","year":"2000","journal-title":"Inform. 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