1. Kotai Antibody Builder: automated high-resolution structural modeling of antibodies.
- Author
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Yamashita K, Ikeda K, Amada K, Liang S, Tsuchiya Y, Nakamura H, Shirai H, and Standley DM
- Subjects
- Complementarity Determining Regions chemistry, Internet, Sequence Alignment, Structural Homology, Protein, Antibodies chemistry, Models, Molecular, Software
- 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., (© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2014
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