{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T09:18:03Z","timestamp":1784366283147,"version":"3.55.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T00:00:00Z","timestamp":1676851200000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation","doi-asserted-by":"crossref","award":["32171442"],"award-info":[{"award-number":["32171442"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation","doi-asserted-by":"crossref","award":["21991082"],"award-info":[{"award-number":["21991082"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation","doi-asserted-by":"crossref","award":["21725506"],"award-info":[{"award-number":["21725506"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation","doi-asserted-by":"crossref","award":["32088101"],"award-info":[{"award-number":["32088101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2018YFA0507703"],"award-info":[{"award-number":["2018YFA0507703"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFA1301603"],"award-info":[{"award-number":["2021YFA1301603"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,2,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Chemical cross-linking combined with mass spectrometry (CXMS) is now a well-established method for profiling existing protein\u2013protein interactions (PPIs) with partially known structures. It is expected to map the results of CXMS with existing structure databases to study the protein dynamic profile in the structure analysis. However, currently available structure-based analysis software suffers from the difficulty of achieving large-scale analysis. Besides, it is infeasible for structure analysis and data mining on a large scale, since of lacking global measurement of dynamic structure mapping results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>ComMap (protein complex structure mapping) is a software designed to perform large-scale structure-based mapping by integrating CXMS data with existing structures. It allows complete the distance calculation of PPIs with existing structures in batch within minutes and provides scores for different PPI-structure pairs of testable hypothetical structural dynamism via a global view.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad077","type":"journal-article","created":{"date-parts":[[2023,2,20]],"date-time":"2023-02-20T13:52:18Z","timestamp":1676901138000},"source":"Crossref","is-referenced-by-count":7,"title":["ComMap: a software to perform large-scale structure-based mapping for cross-linking mass spectrometry"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5720-3130","authenticated-orcid":false,"given":"Weijie","family":"Zhang","sequence":"first","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100039, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yichu","family":"Shan","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lili","family":"Zhao","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100039, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Liang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Engineering Medicine and School of Biological Science and Medical Engineering, Beihang University , Beijing 100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2543-1547","authenticated-orcid":false,"given":"Lihua","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yukui","family":"Zhang","sequence":"additional","affiliation":[{"name":"CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian, Liaoning 116023, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,2,20]]},"reference":[{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1074\/jbc.M116.761841","article-title":"Modeling protein excited-state structures from \u201cover-length\u201d chemical cross-links","volume":"292","author":"Ding","year":"2017","journal-title":"J. Biol. Chem"},{"key":"2023022513303601500_","first-page":"561829","article-title":"xiView: A common platform for the downstream analysis of crosslinking mass spectrometry data","author":"Graham","year":"2019","journal-title":"bioRxiv"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"6953","DOI":"10.1021\/acs.analchem.9b00658","article-title":"First community-wide, comparative cross-linking mass spectrometry study","volume":"91","author":"Iacobucci","year":"2019","journal-title":"Anal. Chem"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1073\/pnas.1902931116","article-title":"High-density chemical cross-linking for modeling protein interactions","volume":"117","author":"Mintseris","year":"2020","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"2863","DOI":"10.1021\/acs.jproteome.6b00274","article-title":"ProXL (protein cross-linking database): A platform for analysis, visualization, and sharing of protein cross-linking mass spectrometry data","volume":"15","author":"Riffle","year":"2016","journal-title":"J. Proteome Res"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"2716","DOI":"10.1093\/bioinformatics\/btw232","article-title":"XLinkDB 2.0: Integrated, large-scale structural analysis of protein crosslinking data","volume":"32","author":"Schweppe","year":"2016","journal-title":"Bioinformatics"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"e2023360118","DOI":"10.1073\/pnas.2023360118","article-title":"Protein interaction landscapes revealed by advanced in vivo cross-linking\u2013mass spectrometry","volume":"118","author":"Wheat","year":"2021","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1021\/acs.analchem.7b04431","article-title":"Cross-linking mass spectrometry: An emerging technology for interactomics and structural biology","volume":"90","author":"Yu","year":"2018","journal-title":"Anal. Chem"},{"key":"2023022513303601500_","doi-asserted-by":"crossref","first-page":"985","DOI":"10.1038\/s41592-020-0959-9","article-title":"Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies","volume":"17","author":"Yugandhar","year":"2020","journal-title":"Nat. Methods"},{"key":"2023022513303601500_","article-title":"SpotLink enables sensitive and precise identification of site nonspecific cross-links at the proteome scale","author":"Zhang","year":"2022","journal-title":"Brief. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad077\/49278178\/btad077.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/2\/btad077\/49334374\/btad077.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/2\/btad077\/49334374\/btad077.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,3,25]],"date-time":"2023-03-25T18:57:15Z","timestamp":1679770635000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad077\/7048661"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,2,1]]},"references-count":10,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2023,2,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad077","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,2,1]]},"published":{"date-parts":[[2023,2,1]]},"article-number":"btad077"}}