Kotai Antibody Builder
Computational Tool
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General Information
DescriptionAutomated high-resolution structural modeling of antibodies
Homepagehttp://kotaiab.org
Publications
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
Kazuo Yamashita; Kazuyoshi Ikeda; Karlou Amada; Shide Liang; Yuko Tsuchiya; Haruki Nakamura; Hiroki Shirai; Daron M. Standley
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
DOI: https://doi.org/10.1093/bioinformatics/btu510
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