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Such movements can impede the identification of structural equivalences when rigid aligners are used.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We introduce a new method called RAPIDO (<jats:underline>R<\/jats:underline> apid <jats:underline>A<\/jats:underline> lignment of <jats:underline>P<\/jats:underline> roteins <jats:underline>i<\/jats:underline> n terms of <jats:underline>Do<\/jats:underline> mains) for the three-dimensional alignment of protein structures in the presence of conformational changes. The flexible aligner is coupled to a genetic algorithm for the identification of structurally conserved regions. RAPIDO is capable of aligning protein structures in the presence of large conformational changes. Structurally conserved regions are reliably detected even if they are discontinuous in sequence but continuous in space and can be used for superpositions revealing subtle differences.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>RAPIDO is more sensitive than other flexible aligners when applied to cases of closely homologues proteins undergoing large conformational changes. When applied to a set of kinase structures it is able to detect similarities that are missed by other alignment algorithms. The algorithm is sufficiently fast to be applied to the comparison of large sets of protein structures.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-9-352","type":"journal-article","created":{"date-parts":[[2008,8,27]],"date-time":"2008-08-27T06:19:26Z","timestamp":1219817966000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":43,"title":["Alignment of protein structures in the presence of domain motions"],"prefix":"10.1186","volume":"9","author":[{"given":"Roberto","family":"Mosca","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Barbara","family":"Brannetti","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas R","family":"Schneider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2008,8,27]]},"reference":[{"issue":"7","key":"2337_CR1","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1002\/pro.5560050711","volume":"5","author":"A Godzik","year":"1996","unstructured":"Godzik A: The structural alignment between two proteins: is there a unique answer? 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