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Updated: Apr 26, 2026
Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy
Published on: August 15, 2014
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
Kazuo Yamashita1, Kazuyoshi Ikeda1, Karlou Amada1
1WPI 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.
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.
Availability And Implementation:
Kotai Antibody Builder is available at http://kotaiab.org
Contact:
standley@ifrec.osaka-u.ac.jp.
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