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Initial alignments are generated by the program Local ASH, and can be supplemented by alignments from any other program.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We compare GASH to DaliLite, CE, and to our earlier program Global ASH on a difficult test set consisting of 3,102 structure pairs, as well as a smaller set derived from the Fischer-Eisenberg set. The extent of alignment crossover, as well as the completeness of the initial set of alignments are examined. The quality of the superpositions is evaluated both by NER and by the number of aligned residues under three different RMSD cutoffs (2,4, and 6\u00c5). In addition to the numerical assessment, the alignments for several biologically related structural pairs are discussed in detail.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>Regardless of which criteria is used to judge the superposition accuracy, GASH achieves the best overall performance, followed by DaliLite, Global ASH, and CE. In terms of CPU usage, DaliLite CE and GASH perform similarly for query proteins under 500 residues, but for larger proteins DaliLite is faster than GASH or CE. Both an http interface and a simple object application protocol (SOAP) interface to the GASH program are available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.pdbj.org\/GASH\/\">http:\/\/www.pdbj.org\/GASH\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/1471-2105-6-221","type":"journal-article","created":{"date-parts":[[2005,9,8]],"date-time":"2005-09-08T18:13:32Z","timestamp":1126203212000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":23,"title":["GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structures"],"prefix":"10.1186","volume":"6","author":[{"given":"Daron M","family":"Standley","sequence":"first","affiliation":[]},{"given":"Hiroyuki","family":"Toh","sequence":"additional","affiliation":[]},{"given":"Haruki","family":"Nakamura","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2005,9,8]]},"reference":[{"key":"546_CR1","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"HM Berman","year":"2000","unstructured":"Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. 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