Publication Date:
2014-11-07
Description:
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
Print ISSN:
1367-4803
Electronic ISSN:
1460-2059
Topics:
Biology
,
Computer Science
,
Medicine
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