{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,24]],"date-time":"2025-10-24T08:24:32Z","timestamp":1761294272599},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,3]],"date-time":"2021-03-03T00:00:00Z","timestamp":1614729600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Brazilian National Research Council"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Chemical cross-linking coupled to mass spectrometry (XLMS) emerged as a powerful technique for studying protein structures and large-scale protein-protein interactions. Nonetheless, XLMS lacks software tailored toward dealing with multiple conformers; this scenario can lead to high-quality identifications that are mutually exclusive. This limitation hampers the applicability of XLMS in structural experiments of dynamic protein systems, where less abundant conformers of the target protein are expected in the sample.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present QUIN-XL, a software that uses unsupervised clustering to group cross-link identifications by their quantitative profile across multiple samples. QUIN-XL highlights regions of the protein or system presenting changes in its conformation when comparing different biological conditions. We demonstrate our software\u2019s usefulness by revisiting the HSP90 protein, comparing three of its different conformers. QUIN-XL\u2019s clusters correlate directly to known protein 3D structures of the conformers and therefore validates our software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>QUIN-XL and a user tutorial are freely available at http:\/\/patternlabforproteomics.org\/quinxl for academic users.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab149","type":"journal-article","created":{"date-parts":[[2021,3,2]],"date-time":"2021-03-02T12:31:22Z","timestamp":1614688282000},"page":"3035-3037","source":"Crossref","is-referenced-by-count":3,"title":["Characterizing protein conformers by cross-linking mass spectrometry and pattern recognition"],"prefix":"10.1093","volume":"37","author":[{"given":"Louise U","family":"Kurt","sequence":"first","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1 81350-010, Brazil"}]},{"given":"Milan A","family":"Clasen","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1 81350-010, Brazil"}]},{"given":"Marlon D M","family":"Santos","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1 81350-010, Brazil"}]},{"given":"Eduardo S B","family":"Lyra","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , S\u00e3o Paulo 13083-862, Brazil"}]},{"given":"Luana O","family":"Santos","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , S\u00e3o Paulo 13083-862, Brazil"}]},{"given":"Carlos H I","family":"Ramos","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , S\u00e3o Paulo 13083-862, Brazil"}]},{"given":"Diogo B","family":"Lima","sequence":"additional","affiliation":[{"name":"Department of Chemical Biology, Leibniz \u2013 Forschungsinstitut f\u00fcr Molekulare Pharmakologie (FMP) , Berlin 13125, Germany"}]},{"given":"Fabio C","family":"Gozzo","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , S\u00e3o Paulo 13083-862, Brazil"}]},{"given":"Paulo C","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Laboratory for Structural and Computational Proteomics, Carlos Chagas Institute , Fiocruz, Paran\u00e1 81350-010, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2021,3,3]]},"reference":[{"key":"2023061310534976300_btab149-B1","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.cbpa.2018.08.006","article-title":"Chemical cross-linking with mass spectrometry: a tool for systems structural biology","volume":"48","author":"Chavez","year":"2019","journal-title":"Curr. 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