{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:29:21Z","timestamp":1762673361369},"reference-count":0,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2004,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Interacting pairs of proteins should co-evolve to maintain functional and structural complementarity. Consequently, such a pair of protein families shows similarity between their phylogenetic trees. Although the tendency of co-evolution has been known for various ligand\u2013receptor pairs, it has not been studied systematically in the widest possible scope. We investigated the degree of co-evolution for more than 900 family pairs in a global protein structural interactome map (PSIMAP\u2014a map of all the structural domain\u2013domain interactions in the PDB).<\/jats:p>\n               <jats:p>Results: There was significant correlation in 45% of the total SCOPs Family level pairs, rising to 78% in 454 reliable family interactions. Expectedly, the intra-molecular interactions between protein families showed stronger co-evolution than inter-molecular interactions. However, both types of interaction have a fundamentally similar pattern of co-evolution except for cases where different interfaces are involved. These results validate the use of co-evolution analysis with predictive methods such as PSIMAP to improve the accuracy of prediction based on \u2018homologous interaction\u2019. The tendency of co-evolution enabled a nearly 5-fold enrichment in the identification of true interactions among the potential interlogues in PSIMAP. The estimated sensitivity was 79.2%, and the specificity was 78.6%.<\/jats:p>\n               <jats:p>Availability: The results of co-evolution analysis are available online at http:\/\/www.biointeraction.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth053","type":"journal-article","created":{"date-parts":[[2004,3,2]],"date-time":"2004-03-02T21:41:06Z","timestamp":1078263666000},"page":"1138-1150","source":"Crossref","is-referenced-by-count":39,"title":["Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP)"],"prefix":"10.1093","volume":"20","author":[{"given":"Wan K.","family":"Kim","sequence":"first","affiliation":[]},{"given":"Dan M.","family":"Bolser","sequence":"additional","affiliation":[]},{"given":"Jong H.","family":"Park","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,2,5]]},"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/7\/1138\/48905353\/bioinformatics_20_7_1138.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/20\/7\/1138\/48905353\/bioinformatics_20_7_1138.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T17:28:35Z","timestamp":1674667715000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/20\/7\/1138\/245685"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,2,5]]},"references-count":0,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2004,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth053","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2004,5,1]]},"published":{"date-parts":[[2004,2,5]]}}}