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Thus, it is highly desirable to develop some computational methods to automatically classify the quaternary structure of proteins from their sequences.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To explore this problem, we adopted an approach based on the functional domain composition of proteins. Every protein was represented by a vector calculated from the domains in the PFAM database. The nearest neighbor algorithm (NNA) was used for classifying the quaternary structure of proteins from this information. The jackknife cross-validation test was performed on the non-redundant protein dataset in which the sequence identity was less than 25%. The overall success rate obtained is 75.17%. Additionally, to demonstrate the effectiveness of this method, we predicted the proteins in an independent dataset and achieved an overall success rate of 84.11%<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Compared with the amino acid composition method and Blast, the results indicate that the domain composition approach may be a more effective and promising high-throughput method in dealing with this complicated problem in bioinformatics.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-7-187","type":"journal-article","created":{"date-parts":[[2006,4,20]],"date-time":"2006-04-20T14:19:38Z","timestamp":1145542778000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Classification of protein quaternary structure by functional domain composition"],"prefix":"10.1186","volume":"7","author":[{"given":"Xiaojing","family":"Yu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chuan","family":"Wang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,4,4]]},"reference":[{"key":"926_CR1","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1016\/B978-0-12-516301-9.50009-7","volume-title":"The Proteins","author":"IM Klotz","year":"1975","unstructured":"Klotz IM, Darnall DW, Langerman NR: Quaternary structure of proteins. 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