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Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/10.life.nctu.edu.tw\/CirPred\/\">http:\/\/10.life.nctu.edu.tw\/CirPred\/<\/jats:ext-link> and <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/lo.life.nctu.edu.tw\/CirPred\/\">http:\/\/lo.life.nctu.edu.tw\/CirPred\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04403-1","type":"journal-article","created":{"date-parts":[[2021,10,13]],"date-time":"2021-10-13T01:26:15Z","timestamp":1634088375000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["CirPred, the first structure modeling and linker design system for circularly permuted proteins"],"prefix":"10.1186","volume":"22","author":[{"given":"Teng-Ruei","family":"Chen","sequence":"first","affiliation":[]},{"given":"Yen-Cheng","family":"Lin","sequence":"additional","affiliation":[]},{"given":"Yu-Wei","family":"Huang","sequence":"additional","affiliation":[]},{"given":"Chih-Chieh","family":"Chen","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8865-5113","authenticated-orcid":false,"given":"Wei-Cheng","family":"Lo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,10,12]]},"reference":[{"issue":"3","key":"4403_CR1","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1016\/S0959-440X(97)80061-9","volume":"7","author":"Y Lindqvist","year":"1997","unstructured":"Lindqvist Y, Schneider G. 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