{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T07:52:37Z","timestamp":1778053957247,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Kotai Antibody Builder is a Web service for tertiary structural modeling of antibody variable regions. It consists of three main steps: hybrid template selection by sequence alignment and canonical rules, 3D rendering of alignments and CDR-H3 loop modeling. For the last step, in addition to rule-based heuristics used to build the initial model, a refinement option is available that uses fragment assembly followed by knowledge-based scoring. Using targets from the Second Antibody Modeling Assessment, we demonstrate that Kotai Antibody Builder generates models with an overall accuracy equal to that of the best-performing semi-automated predictors using expert knowledge.<\/jats:p>\n               <jats:p>Availability and implementation: Kotai Antibody Builder is available at http:\/\/kotaiab.org<\/jats:p>\n               <jats:p>Contact: \u00a0standley@ifrec.osaka-u.ac.jp<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu510","type":"journal-article","created":{"date-parts":[[2014,7,27]],"date-time":"2014-07-27T00:29:24Z","timestamp":1406420964000},"page":"3279-3280","source":"Crossref","is-referenced-by-count":49,"title":["Kotai Antibody Builder: automated high-resolution structural modeling of antibodies"],"prefix":"10.1093","volume":"30","author":[{"given":"Kazuo","family":"Yamashita","sequence":"first","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuyoshi","family":"Ikeda","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karlou","family":"Amada","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shide","family":"Liang","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuko","family":"Tsuchiya","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Haruki","family":"Nakamura","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, 2 National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, 3 Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and 4 Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroki","family":"Shirai","sequence":"additional","affiliation":[{"name":"1 WPI Immunology Frontier 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