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Given two proteins, the algorithm first identifies all pairs of structurally similar fragments and subsequently clusters into larger units pairs of fragments that are compatible in three dimensions. The detection of similar substructures is independent of insertion\/deletion penalties and can be chosen to be independent of the topology of loop connections and to allow for reversal of chain direction. Using distance geometry filters and other approximations, the algorithm, implemented in the WHAT IF program, is so fast that structural comparison of a single protein with the entire database of known protein structures can be performed routinely on a workstation. The method reproduces known non\u2010trivial superpositions such as plastocyanin on azurin. In addition, we report surprising structural similarity between ubiquitin and a (2Fe\u20102S) ferredoxin.<\/jats:p>","DOI":"10.1002\/prot.340110107","type":"journal-article","created":{"date-parts":[[2005,5,29]],"date-time":"2005-05-29T01:11:38Z","timestamp":1117329098000},"page":"52-58","source":"Crossref","is-referenced-by-count":158,"title":["Detection of common three\u2010dimensional substructures in proteins"],"prefix":"10.1002","volume":"11","author":[{"given":"Gerrit","family":"Vriend","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2004,2,3]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(78)90207-3"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/0076-6879(90)83044-A"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(80)90373-3"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/2.8.589"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(90)90087-3"},{"key":"e_1_2_1_7_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0567739478001680"},{"key":"e_1_2_1_8_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(89)90084-3"},{"key":"e_1_2_1_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(90)90134-8"},{"key":"e_1_2_1_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02458836"},{"key":"e_1_2_1_11_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0108767384001239"},{"key":"e_1_2_1_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(80)90357-5"},{"key":"e_1_2_1_13_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.75.5.2180"},{"key":"e_1_2_1_14_2","doi-asserted-by":"publisher","DOI":"10.1145\/359094.359095"},{"key":"e_1_2_1_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/0263-7855(89)80056-6"},{"key":"e_1_2_1_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0263-7855(98)80002-7"},{"key":"e_1_2_1_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(76)90195-9"},{"key":"e_1_2_1_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(73)90388-4"},{"key":"e_1_2_1_19_2","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.1988.10506469"},{"key":"e_1_2_1_20_2","doi-asserted-by":"publisher","DOI":"10.1080\/07391102.1989.10506535"},{"key":"e_1_2_1_21_2","doi-asserted-by":"publisher","DOI":"10.1002\/j.1460-2075.1986.tb04287.x"},{"key":"e_1_2_1_22_2","doi-asserted-by":"publisher","DOI":"10.1002\/bip.360221211"},{"key":"e_1_2_1_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(84)90472-8"},{"key":"e_1_2_1_24_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(83)80064-3"},{"key":"e_1_2_1_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(88)90129-5"},{"key":"e_1_2_1_26_2","unstructured":"1985 Verlag Chemie Weinheim Adman E. 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