title: Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Kotai Antibody Builder is available at http://kotaiab.org
  
  
  BACKGROUND
  standley@ifrec.osaka-u.ac.jp.
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Kazuo
authors: K
authors: Yamashita
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Kazuyoshi
authors: K
authors: Ikeda
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Karlou
authors: K
authors: Amada
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Shide
authors: S
authors: Liang
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Yuko
authors: Y
authors: Tsuchiya
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Haruki
authors: H
authors: Nakamura
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Hiroki
authors: H
authors: Shirai
authors: WPI Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka 565-0871, National Institute of Biomedical Innovation, Ibaraki City, Osaka 567-0085, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871 and Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki 305-8585, Japan.
authors: Daron M
authors: DM
authors: Standley
mesh_terms: D000906:Antibodies / Q000737:chemistry*; D022801:Complementarity Determining Regions / Q000737:chemistry; D020407:Internet; D008958:Models, Molecular; D016415:Sequence Alignment; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D000906:Antibodies; D022801:Complementarity Determining Regions