{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:34:55Z","timestamp":1761744895704},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,10]],"date-time":"2019-01-10T00:00:00Z","timestamp":1547078400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"agency Fapesp","award":["2010\/16947-9","2013\/05475-7","2013\/08293-7","2016\/13195-2","2018\/14274-9"],"award-info":[{"award-number":["2010\/16947-9","2013\/05475-7","2013\/08293-7","2016\/13195-2","2018\/14274-9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>A software was developed to evaluate structural models using chemical crosslinking experiments. The user provides the types of linkers used and their reactivity, and the observed crosslinks and dead-ends. The software computes the minimum length of a physically inspired linker that connects the reactive atoms of interest, and reports the consistency of each distance with the experimental observation. Statistics on model consistency with the links are provided. Tools to evaluate the correlation of crosslinks in ensembles of models were developed. TopoLink was used to evaluate the potential crosslinks of all structures of the CATH database. The number of crosslinks expected as a function of protein size and linker length can be used as guide for experimental design.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TopoLink is available as free software at http:\/\/m3g.iqm.unicamp.br\/topolink, and distributed as source code with a user-friendly graphical interface for Windows. A web server is also provided.<\/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\/btz014","type":"journal-article","created":{"date-parts":[[2019,1,4]],"date-time":"2019-01-04T20:11:19Z","timestamp":1546632679000},"page":"3169-3170","source":"Crossref","is-referenced-by-count":20,"title":["TopoLink: evaluation of structural models using chemical crosslinking distance constraints"],"prefix":"10.1093","volume":"35","author":[{"given":"Allan J R","family":"Ferrari","sequence":"first","affiliation":[{"name":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil"}]},{"given":"Milan A","family":"Clasen","sequence":"additional","affiliation":[{"name":"Carlos Chagas Institute , Fiocruz, Brazil"}]},{"given":"Louise","family":"Kurt","sequence":"additional","affiliation":[{"name":"Carlos Chagas Institute , Fiocruz, Brazil"}]},{"given":"Paulo C","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Carlos Chagas Institute , Fiocruz, Brazil"}]},{"given":"Fabio C","family":"Gozzo","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil"}]},{"given":"Leandro","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas , Campinas, SP, Brazil"},{"name":"Center for Computing in Engineering & Sciences, University of Campinas , Campinas, SP, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2019,1,10]]},"reference":[{"key":"2023062711310411700_btz014-B1","doi-asserted-by":"crossref","first-page":"1751","DOI":"10.1016\/j.str.2017.08.015","article-title":"Accommodating protein dynamics in the modeling of chemical crosslinks","volume":"25","author":"Degiacomi","year":"2017","journal-title":"Structure"},{"key":"2023062711310411700_btz014-B2","doi-asserted-by":"crossref","first-page":"2201","DOI":"10.1093\/bioinformatics\/bty074","article-title":"Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals","volume":"34","author":"Dos Santos","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062711310411700_btz014-B3","doi-asserted-by":"crossref","first-page":"2163","DOI":"10.1093\/bioinformatics\/btr348","article-title":"Xwalk: computing and visualizing distances in cross-linking experiments","volume":"27","author":"Kahraman","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062711310411700_btz014-B4","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1074\/mcp.M116.058560","article-title":"The importance of non-accessible crosslinks and solvent accessible surface distance in modeling proteins with restraints from crosslinking mass spectrometry","volume":"15","author":"Matthew Allen Bullock","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"key":"2023062711310411700_btz014-B5","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/j.tibs.2017.12.006","article-title":"Protein tertiary structure by crosslinking\/mass spectrometry","volume":"43","author":"Schneider","year":"2018","journal-title":"Trends Biochem. Sci"},{"key":"2023062711310411700_btz014-B6","doi-asserted-by":"crossref","first-page":"D376","DOI":"10.1093\/nar\/gku947","article-title":"CATH: comprehensive structural and functional annotations for genome sequences","volume":"43","author":"Sillitoe","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023062711310411700_btz014-B7","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"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3169\/50719831\/bioinformatics_35_17_3169.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3169\/50719831\/bioinformatics_35_17_3169.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:32:05Z","timestamp":1687865525000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3169\/5284905"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,10]]},"references-count":7,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz014","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,10]]}}}