{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:18Z","timestamp":1740185118187,"version":"3.37.3"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,12,4]],"date-time":"2019-12-04T00:00:00Z","timestamp":1575417600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"General Research Fund of the Hong Kong Research Grants Council","award":["16202918"],"award-info":[{"award-number":["16202918"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Patterns of mutational correlations, learnt from protein sequences, have been shown to be informative of co-evolutionary sectors that are tightly linked to functional and\/or structural properties of proteins. Previously, we developed a statistical inference method, robust co-evolutionary analysis (RoCA), to reliably predict co-evolutionary sectors of proteins, while controlling for statistical errors caused by limited data. RoCA was demonstrated on multiple viral proteins, with the inferred sectors showing close correspondences with experimentally-known biochemical domains. To facilitate seamless use of RoCA and promote more widespread application to protein data, here we present a standalone cross-platform package \u2018RocaSec\u2019 which features an easy-to-use GUI. The package only requires the multiple sequence alignment of a protein for inferring the co-evolutionary sectors. In addition, when information on the protein biochemical domains is provided, RocaSec returns the corresponding statistical association between the inferred sectors and biochemical domains.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The RocaSec software is publicly available under the MIT License at https:\/\/github.com\/ahmedaq\/RocaSec.<\/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\/btz890","type":"journal-article","created":{"date-parts":[[2019,12,2]],"date-time":"2019-12-02T20:50:36Z","timestamp":1575319836000},"page":"2262-2263","source":"Crossref","is-referenced-by-count":1,"title":["RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5295-9067","authenticated-orcid":false,"given":"Ahmed A","family":"Quadeer","sequence":"first","affiliation":[{"name":"Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology , Hong Kong, China"}]},{"given":"David","family":"Morales-Jimenez","sequence":"additional","affiliation":[{"name":"Institute of Electronics, Communications and Information Technology, Queen\u2019s University Belfast , NI Science Park, Queens Road, Belfast BT3 9DT, UK"}]},{"given":"Matthew R","family":"McKay","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology , Hong Kong, China"},{"name":"Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology , Hong Kong, China"}]}],"member":"286","published-online":{"date-parts":[[2019,12,4]]},"reference":[{"key":"2023062300073477600_btz890-B1","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.str.2012.01.010","article-title":"The Protein Data Bank at 40: reflecting on the past to prepare for the future","volume":"20","author":"Berman","year":"2012","journal-title":"Structure"},{"key":"2023062300073477600_btz890-B2","doi-asserted-by":"crossref","first-page":"11530","DOI":"10.1073\/pnas.1105315108","article-title":"Coordinate linkage of HIV evolution reveals regions of immunological vulnerability","volume":"108","author":"Dahirel","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062300073477600_btz890-B4","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nrg3414","article-title":"Emerging methods in protein co-evolution","volume":"14","author":"de Juan","year":"2013","journal-title":"Nat. Rev. Genet"},{"key":"2023062300073477600_btz890-B5","doi-asserted-by":"crossref","first-page":"e1006409","DOI":"10.1371\/journal.pcbi.1006409","article-title":"Co-evolution networks of HIV\/HCV are modular with direct association to structure and function","volume":"14","author":"Quadeer","year":"2018","journal-title":"PLoS Comput. Biol"},{"key":"2023062300073477600_btz890-B6","doi-asserted-by":"crossref","first-page":"7628","DOI":"10.1128\/JVI.03812-13","article-title":"Statistical linkage analysis of substitutions in patient-derived sequences of genotype 1a hepatitis C virus nonstructural protein 3 exposes targets for immunogen design","volume":"88","author":"Quadeer","year":"2014","journal-title":"J. Virol"},{"key":"2023062300073477600_btz890-B7","doi-asserted-by":"crossref","first-page":"e1004817","DOI":"10.1371\/journal.pcbi.1004817","article-title":"Evolution-based functional decomposition of proteins","volume":"12","author":"Rivoire","year":"2016","journal-title":"PLoS Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz890\/31509690\/btz890.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/7\/2262\/50670490\/bioinformatics_36_7_2262.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/7\/2262\/50670490\/bioinformatics_36_7_2262.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,23]],"date-time":"2023-06-23T03:01:24Z","timestamp":1687489284000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/7\/2262\/5652092"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,12,4]]},"references-count":6,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2020,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz890","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2020,4,1]]},"published":{"date-parts":[[2019,12,4]]}}}