Kazuo Yamashita1, Kazuyoshi Ikeda1, Karlou Amada1, Shide Liang1, Yuko Tsuchiya1, Haruki Nakamura1, Hiroki Shirai1, Daron M Standley1. 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.
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.
Authors: Katerina C Nastou; Eleftheria G Karataraki; Nikos C Papandreou; Anna-Isavella G Rerra; Vassiliki P Grimanelli; Ilias Maglogiannis; Stavros J Hamodrakas; Vassiliki A Iconomidou Journal: Adv Exp Med Biol Date: 2020 Impact factor: 2.622
Authors: Brian D Weitzner; Jeliazko R Jeliazkov; Sergey Lyskov; Nicholas Marze; Daisuke Kuroda; Rahel Frick; Jared Adolf-Bryfogle; Naireeta Biswas; Roland L Dunbrack; Jeffrey J Gray Journal: Nat Protoc Date: 2017-01-26 Impact factor: 13.491
Authors: Michael Schantz Klausen; Mads Valdemar Anderson; Martin Closter Jespersen; Morten Nielsen; Paolo Marcatili Journal: Nucleic Acids Res Date: 2015-05-24 Impact factor: 16.971
Authors: James Dunbar; Konrad Krawczyk; Jinwoo Leem; Claire Marks; Jaroslaw Nowak; Cristian Regep; Guy Georges; Sebastian Kelm; Bojana Popovic; Charlotte M Deane Journal: Nucleic Acids Res Date: 2016-04-29 Impact factor: 16.971