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Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-11-303","type":"journal-article","created":{"date-parts":[[2010,6,3]],"date-time":"2010-06-03T18:16:00Z","timestamp":1275588960000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":40,"title":["Detecting internally symmetric protein structures"],"prefix":"10.1186","volume":"11","author":[{"given":"Changhoon","family":"Kim","sequence":"first","affiliation":[]},{"given":"Jodi","family":"Basner","sequence":"additional","affiliation":[]},{"given":"Byungkook","family":"Lee","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,6,3]]},"reference":[{"issue":"2-3","key":"3760_CR1","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1006\/jsbi.2001.4392","volume":"134","author":"MA Andrade","year":"2001","unstructured":"Andrade MA, Perez-Iratxeta C, Ponting CP: Protein repeats: structures, functions, and evolution. 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