{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:15:28Z","timestamp":1767960928735,"version":"3.49.0"},"reference-count":43,"publisher":"Oxford University Press (OUP)","issue":"17","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Ideally, only proteins that exhibit highly similar domain architectures should be compared with one another as homologues or be classified into a single family. By combining three different indices, the Jaccard index, the Goodman-Kruskal \u03b3 function and the domain duplicate index, into a single similarity measure, we propose a method for comparing proteins based on their domain architectures.<\/jats:p>\n               <jats:p>Results: Evaluation of the method using the eukaryotic orthologous groups of proteins (KOGs) database indicated that it allows the automatic and efficient comparison of multiple-domain proteins, which are usually refractory to classic approaches based on sequence similarity measures. As a case study, the PDZ and LRR_1 domains are used to demonstrate how proteins containing promiscuous domains can be clearly compared using our method. For the convenience of users, a web server was set up where three different query interfaces were implemented to compare different domain architectures or proteins with domain(s), and to identify the relationships among domain architectures within a given KOG from the Clusters of Orthologous Groups of Proteins database.<\/jats:p>\n               <jats:p>Conclusion: The approach we propose is suitable for estimating the similarity of domain architectures of proteins, especially those of multidomain proteins.<\/jats:p>\n               <jats:p>Availability: \u00a0<\/jats:p>\n               <jats:p>Contact: \u00a0linkui@bnu.edu.cn<\/jats:p>\n               <jats:p>Supplementary Information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl366","type":"journal-article","created":{"date-parts":[[2006,7,13]],"date-time":"2006-07-13T00:39:14Z","timestamp":1152751154000},"page":"2081-2086","source":"Crossref","is-referenced-by-count":48,"title":["An initial strategy for comparing proteins at the domain architecture level"],"prefix":"10.1093","volume":"22","author":[{"given":"Kui","family":"Lin","sequence":"first","affiliation":[{"name":"MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University \u00a0 Beijing 100875, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lei","family":"Zhu","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University \u00a0 Beijing 100875, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Da-Yong","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory for Biodiversity Science and Ecological Engineering and College of Life Sciences, Beijing Normal University \u00a0 Beijing 100875, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,7,12]]},"reference":[{"key":"2023012409153503300_b1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"2023012409153503300_b2","doi-asserted-by":"crossref","first-page":"D226","DOI":"10.1093\/nar\/gkh039","article-title":"SCOP database in 2004: refinements integrate structure and sequence family data","volume":"32","author":"Andreeva","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409153503300_b3","doi-asserted-by":"crossref","first-page":"S83","DOI":"10.1093\/bioinformatics\/17.suppl_1.S83","article-title":"An insight into domain combinations","volume":"17","author":"Apic","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012409153503300_b4","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1093\/nar\/30.1.276","article-title":"The Pfam protein families database","volume":"30","author":"Bateman","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012409153503300_b5","doi-asserted-by":"crossref","first-page":"D138","DOI":"10.1093\/nar\/gkh121","article-title":"The Pfam protein families database","volume":"32","author":"Bateman","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012409153503300_b6","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/ng0498-313","article-title":"Predicting functions from protein sequences\u2014where are the bottlenecks?","volume":"18","author":"Bork","year":"1998","journal-title":"Nat. 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