{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T00:16:14Z","timestamp":1780877774762,"version":"3.54.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The technique of chemical cross-linking followed by mass spectrometry has proven to bring valuable information about the protein structure and interactions between proteic subunits. It is an effective and efficient way to experimentally investigate some aspects of a protein structure when NMR and X-ray crystallography data are lacking.<\/jats:p>\n               <jats:p>Results: We introduce MSX-3D, a tool specifically geared to validate protein models using mass spectrometry. In addition to classical peptides identifications, it allows an interactive 3D visualization of the distance constraints derived from a cross-linking experiment.<\/jats:p>\n               <jats:p>Availability: Freely available at http:\/\/proteomics-pbil.ibcp.fr<\/jats:p>\n               <jats:p>Contact: \u00a0g.deleage@ibcp.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn510","type":"journal-article","created":{"date-parts":[[2008,10,1]],"date-time":"2008-10-01T02:32:45Z","timestamp":1222828365000},"page":"2782-2783","source":"Crossref","is-referenced-by-count":17,"title":["MSX-3D: a tool to validate 3D protein models using mass spectrometry"],"prefix":"10.1093","volume":"24","author":[{"given":"Micha\u00ebl","family":"Heymann","sequence":"first","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Paramelle","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilles","family":"Subra","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Forest","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean","family":"Martinez","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Geourjon","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gilbert","family":"Del\u00e9age","sequence":"additional","affiliation":[{"name":"1 Institut de Biologie et Chimie des Prot\u00e9ines (IBCP) UMR5086 CNRS, Universit\u00e9 Lyon 1, IFR128 BioSciences Lyon-Gerland, 7 passage du Vercors 69367 Lyon cedex 07, 2Institut des Biomol\u00e9cules Max Mousseron (IBMM), UMR5247 CNRS, Universit\u00e9s Montpellier 1 et 2, 15 avenue Charles Flahault, 34000 Montpellier and 3Protein Mass Spectrometry Laboratory, Institut de Biologie Structurale, UMR5075 CEA, CNRS, UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 1, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,9,30]]},"reference":[{"key":"2023020212242304000_B1","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1093\/bioinformatics\/18.1.213","article-title":"Geno3D: automatic comparative molecular modelling of protein","volume":"18","author":"Combet","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020212242304000_B2","doi-asserted-by":"crossref","first-page":"2145","DOI":"10.1021\/ac051339c","article-title":"Pro-CrossLink. Software tool for protein cross-linking and mass spectrometry","volume":"78","author":"Gao","year":"2006","journal-title":"Anal. Chem."},{"key":"2023020212242304000_B3","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1039\/b801810c","article-title":"Mass spectrometric analysis of cross-linking sites for the structure of proteins and protein complexes","volume":"4","author":"Lee","year":"2008","journal-title":"Mol. Biosyst."},{"key":"2023020212242304000_B4","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/j.1742-4658.2005.05053.x","article-title":"Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes","volume":"273","author":"de Koning","year":"2006","journal-title":"FEBS J."},{"key":"2023020212242304000_B5","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1016\/S1044-0305(03)00327-1","article-title":"MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides","volume":"14","author":"Schilling","year":"2003","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023020212242304000_B6","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1002\/mas.20082","article-title":"Chemical cross-linking and mass spectrometry to map three-dimensional protein structures and protein-protein interactions","volume":"25","author":"Sinz","year":"2006","journal-title":"Mass Spectrom. Rev."},{"key":"2023020212242304000_B7","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1021\/ac051634x","article-title":"SearchXLinks. A program for the identification of disulfide bonds in proteins from mass spectra","volume":"78","author":"Wefing","year":"2006","journal-title":"Anal. Chem."},{"key":"2023020212242304000_B8","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1038\/38775","article-title":"Haem-ligand switching during catalysis in crystals of a nitrogen-cycle enzyme","volume":"389","author":"Williams","year":"1997","journal-title":"Nature"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/23\/2782\/49056191\/bioinformatics_24_23_2782.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/23\/2782\/49056191\/bioinformatics_24_23_2782.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T15:05:51Z","timestamp":1675350351000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/23\/2782\/180068"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,9,30]]},"references-count":8,"journal-issue":{"issue":"23","published-print":{"date-parts":[[2008,12,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn510","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,12,1]]},"published":{"date-parts":[[2008,9,30]]}}}