{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T16:29:55Z","timestamp":1787502595523,"version":"build-2736575974"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T00:00:00Z","timestamp":1683158400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["469281184"],"award-info":[{"award-number":["469281184"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The development of AlphaFold for protein structure prediction has opened a new era in structural biology. This is even more the case for AlphaFold-Multimer for the prediction of protein complexes. The interpretation of these predictions has become more important than ever, but it is difficult for the non-specialist. While an evaluation of the prediction quality is provided for monomeric protein predictions by the AlphaFold Protein Structure Database, such a tool is missing for predicted complex structures. Here, we present the PAE Viewer webserver (http:\/\/www.subtiwiki.uni-goettingen.de\/v4\/paeViewerDemo), an online tool for the integrated visualization of predicted protein complexes using a 3D structure display combined with an interactive representation of the Predicted Aligned Error (PAE). This metric allows an estimation of the quality of the prediction. Importantly, our webserver also allows the integration of experimental cross-linking data which helps to interpret the reliability of the structure predictions. With the PAE Viewer, the user obtains a unique online tool which for the first time allows the intuitive evaluation of the PAE for protein complex structure predictions with integrated crosslinks.<\/jats:p>","DOI":"10.1093\/nar\/gkad350","type":"journal-article","created":{"date-parts":[[2023,5,4]],"date-time":"2023-05-04T08:25:35Z","timestamp":1683188735000},"page":"W404-W410","source":"Crossref","is-referenced-by-count":216,"title":["PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks"],"prefix":"10.1093","volume":"51","author":[{"given":"Christoph","family":"Elfmann","sequence":"first","affiliation":[{"name":"Department of General Microbiology, Georg-August-University G\u00f6ttingen , GZMB, 37077\u00a0 G\u00f6ttingen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5881-5390","authenticated-orcid":false,"given":"J\u00f6rg","family":"St\u00fclke","sequence":"additional","affiliation":[{"name":"Department of General Microbiology, Georg-August-University G\u00f6ttingen , GZMB, 37077\u00a0 G\u00f6ttingen , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,4]]},"reference":[{"key":"2023070504582491300_B1","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1021\/cr040409x","article-title":"Principles of protein\u2212protein interactions: what are the preferred ways for proteins to interact?","volume":"108","author":"Keskin","year":"2008","journal-title":"Chem. Rev."},{"key":"2023070504582491300_B2","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1385\/1-59259-762-9:003","article-title":"Structural basis of protein-protein interactions","volume-title":"Protein-Protein Interactions","author":"Liddington","year":"2004"},{"key":"2023070504582491300_B3","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1126\/science.abb3758","article-title":"In-cell architecture of an actively transcribing-translating expressome","volume":"369","author":"O\u2019Reilly","year":"2020","journal-title":"Science"},{"key":"2023070504582491300_B4","doi-asserted-by":"crossref","first-page":"e11544","DOI":"10.15252\/msb.202311544","article-title":"Protein complexes in cells by AI-assisted structural proteomics","volume":"19","author":"O\u2019Reilly","year":"2023","journal-title":"Mol. Syst. Biol."},{"key":"2023070504582491300_B5","doi-asserted-by":"crossref","first-page":"774","DOI":"10.1038\/s41592-022-01454-x","article-title":"Understudied proteins: opportunities and challenges for functional proteomics","volume":"19","author":"Kustatscher","year":"2022","journal-title":"Nat. Methods"},{"key":"2023070504582491300_B6","doi-asserted-by":"crossref","DOI":"10.1111\/mmi.15053","article-title":"Understudied proteins and understudied functions in the model bacterium Bacillus subtilis \u2013 a major challenge in current research","author":"Wicke","year":"2023","journal-title":"Mol. Microbiol."},{"key":"2023070504582491300_B7","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023070504582491300_B8","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504582491300_B9","doi-asserted-by":"crossref","DOI":"10.1101\/2021.10.04.463034","article-title":"Protein complex prediction with AlphaFold-multimer","author":"Evans","year":"2021"},{"key":"2023070504582491300_B10","doi-asserted-by":"crossref","first-page":"6028","DOI":"10.1038\/s41467-022-33729-4","article-title":"Predicting the structure of large protein complexes using AlphaFold and Monte Carlo tree search","volume":"13","author":"Bryant","year":"2022","journal-title":"Nat. Commun."},{"key":"2023070504582491300_B11","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41592-022-01488-1","article-title":"ColabFold: making protein folding accessible to all","volume":"19","author":"Mirdita","year":"2022","journal-title":"Nat. Methods"},{"key":"2023070504582491300_B12","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1002\/pro.3943","article-title":"UCSF ChimeraX: structure visualization for researchers, educators, and developers","volume":"30","author":"Pettersen","year":"2021","journal-title":"Protein Sci."},{"key":"2023070504582491300_B13","doi-asserted-by":"crossref","first-page":"D875","DOI":"10.1093\/nar\/gkab943","article-title":"The current state of SubtiWiki, the database for the model organism Bacillus subtilis","volume":"50","author":"Pedreira","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504582491300_B14","doi-asserted-by":"crossref","first-page":"2722","DOI":"10.1093\/bioinformatics\/btt473","article-title":"lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests","volume":"29","author":"Mariani","year":"2013","journal-title":"Bioinformatics"},{"key":"2023070504582491300_B15","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1002\/prot.20264","article-title":"Scoring function for automated assessment of protein structure template quality","volume":"57","author":"Zhang","year":"2004","journal-title":"Proteins"},{"key":"2023070504582491300_B16","doi-asserted-by":"crossref","first-page":"3755","DOI":"10.1093\/bioinformatics\/bty419","article-title":"NGL viewer: web-based molecular graphics for large complexes","volume":"34","author":"Rose","year":"2018","journal-title":"Bioinformatics"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W404\/50736556\/gkad350.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W404\/50736556\/gkad350.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T05:35:58Z","timestamp":1688535358000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W404\/7151339"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5,4]]},"references-count":16,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,5,4]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad350","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,5,4]]}}}