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Bioinformatics. 2014 Nov 15;30(22):3279-80. doi: 10.1093/bioinformatics/btu510. Epub 2014 Jul 26.

Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.

Author information

1
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.

Abstract

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.

PMID:
25064566
DOI:
10.1093/bioinformatics/btu510
[Indexed for MEDLINE]
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