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Modern computational and experimental methodologies, such as molecular coevolution and chemical cross-linking mass-spectrometry allowed protein structural characterization to previously intangible systems. Despite several independent successful examples, data from these distinct methodologies have not been systematically studied in conjunction. One challenge of structural inference using coevolution is that it is limited to sequence fragments within a conserved and unique domain for which sufficient sequence datasets are available. Therefore, coupling coevolutionary data with complimentary distance constraints from orthogonal sources can provide additional precision to structure prediction methodologies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we present a methodology to combine residue interaction data obtained from coevolutionary information and cross-linking\/mass spectrometry distance constraints in order to identify functional states of proteins. Using a combination of structure-based models (SBMs) with optimized Gaussian-like potentials, secondary structure estimation and simulated annealing molecular dynamics, we provide an automated methodology to integrate constraint data from diverse sources in order to elucidate the native conformation of full protein systems with distinct complexity and structural topologies. We show that cross-linking mass spectrometry constraints improve the structure predictions obtained from SBMs and coevolution signals, and that the constraints obtained by each method have a useful degree of complementarity that promotes enhanced fold estimates.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Scripts and procedures to implement the methodology presented herein are available at https:\/\/github.com\/mcubeg\/DCAXL.<\/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\/bty074","type":"journal-article","created":{"date-parts":[[2018,2,10]],"date-time":"2018-02-10T20:08:39Z","timestamp":1518293319000},"page":"2201-2208","source":"Crossref","is-referenced-by-count":18,"title":["Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3315-747X","authenticated-orcid":false,"given":"Ricardo N","family":"dos Santos","sequence":"first","affiliation":[{"name":"Institute of Chemistry, University of Campinas, Campinas, Brazil"},{"name":"Center for Computational Engineering and Sciences, University of Campinas, Campinas, Brazil"}]},{"given":"Allan J R","family":"Ferrari","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas, Campinas, Brazil"}]},{"given":"Hugo C R","family":"de Jesus","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas, Campinas, Brazil"}]},{"given":"F\u00e1bio C","family":"Gozzo","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas, Campinas, Brazil"}]},{"given":"Faruck","family":"Morcos","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Texas at Dallas, Richardson, USA"}]},{"given":"Leandro","family":"Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Institute of Chemistry, University of Campinas, Campinas, Brazil"},{"name":"Center for Computational Engineering and Sciences, University of Campinas, Campinas, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2018,2,12]]},"reference":[{"key":"2023051604100058600_bty074-B1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S0092-8674(00)80922-8","article-title":"The cell as a collection of protein machines: preparing the next generation of molecular biologists","volume":"92","author":"Alberts","year":"1998","journal-title":"Cell"},{"key":"2023051604100058600_bty074-B2","author":"Alberts","year":"2014"},{"key":"2023051604100058600_bty074-B3","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1126\/science.181.4096.223","article-title":"Principles that govern the folding of protein chains","volume":"181","author":"Anfinsen","year":"1973","journal-title":"Science"},{"key":"2023051604100058600_bty074-B4","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1042\/BST20130055","article-title":"Centenary award and Sir Frederick gowland hopkins memorial lecture. 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