Kuroda Daisuke

クロダダイスケ | Kuroda Daisuke

Affiliation and department：
Job title： Senior Scientist
Homepage URL (2)： https://scholar.google.com/citations?hl=jp&user=3nTWsxcAAAAJ , https://scholar.google.com/citations?hl=en&user=3nTWsxcAAAAJ

Research field (7)： Immunology , Biological, health, and medical informatics , Systems genomics , Structural biochemistry , Intelligent informatics , Soft computing , Chemical biology

Research keywords (13)： Computational science , Antibody , Vaccine , Bioinformatics , Computational Design , Infectious disease , Biophysical chemistry , Informatics , Quantum Chemistry , Genome Science , Synthetic Biology , Systems Biology , Infectious immunology

Research theme for competitive and other funds (19)：

2022 - 2028 Evolution of humoral immune memory for resisting viral escape
2023 - 2026 Study of brain organoids and mouse models for the therapeutic application of paramyxovirus central nervous system infection
2021 - 2025 Transporting drugs across the blood-brain barrier through information technology
2023 - 2024 Development of molecular design and screening method of broadly neutralizing antibodies using structural information
2021 - 2024 Development of computing/information platform for analysis of B-cell repertoires associated with infectious diseases

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Papers (59)：

Koichi Yamamoto, Satoru Nagatoishi, Makoto Nakakido, Daisuke Kuroda, Kouhei Tsumoto. Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain VHH antibodies. Biochemical and Biophysical Research Communications. 2024
Akinobu Senoo, Masato Hoshino, Toshiki Shiomi, Makoto Nakakido, Satoru Nagatoishi, Daisuke Kuroda, Ichiro Nakagawa, Jeremy R. H. Tame, Jose M. M. Caaveiro, Kouhei Tsumoto. Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes. Scientific Reports. 2024. 14. 1
Rimpa Paul, Keisuke Kasahara, Jiei Sasaki, Jorge Fernández Pérez, Ryo Matsunaga, Takao Hashiguchi, Daisuke Kuroda, Kouhei Tsumoto. Unveiling the affinity-stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction. Frontiers in Molecular Biosciences. 2024. 10
Traian Sulea, Sandeep Kumar, Daisuke Kuroda. Editorial: Progress and challenges in computational structure-based design and development of biologic drugs. Frontiers in Molecular Biosciences. 2024. 11
Taichi Sumikawa, Makoto Nakakido, Ryo Matsunaga, Daisuke Kuroda, Satoru Nagatoishi, Kouhei Tsumoto. Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen. Journal of Biological Chemistry. 2024. 300. 2. 105640-105640

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MISC (8)：

Daisuke Kuroda, Yoshimasa Takahashi. Current status of computer-aided immunogen design. BIO Clinica. 2024. 印刷中
Daisuke Kuroda. Computer-aided design of antibodies and vaccine immunogens. Frontier. 2023. 5. 1. 2-12
Daisuke Kuroda. Computer-aided antibody design. Experimental Medichine. 2022. 40. 20. 122-129
Daisuke Kuroda. Modeling antibody structure through computational chemistry. SAR News. 2022. 43. 9-23
黒田大祐, 津本浩平. 【構造生命科学による創薬への挑戦】タンパク質工学から創薬へ立体構造から眺めるSARS-CoV-2中和抗体. 医学のあゆみ. 2021. 278. 6. 609-615

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Books (4)：

Computer-Aided Antibody Design (Methods in Molecular Biology, 2552)
2022 ISBN:1071626086
The Perfect Manual Interaction Analysis for Drug Discovery
Yodosha 2021 ISBN:4758122563
Frontier of Antibody Engineering for Next-generation Therapeutics
CMC Publishing CO.,LTD. 2012 ISBN:9784781306735
Computational Biology: New Research
Nova Science Publishers, Inc. 2009 ISBN:9781606920404

Lectures and oral presentations (29)：

In silico evolution of SARS-CoV-2 antibodies in humans increases the resilience against emerging Omicron subvariants
(The 52nd Annual Meeting of the Japanese Society for Immunology 2024)
Computer-aided antibody design in the era of AlphaFold
(the 103rd CSJ Annual Meeting (2023) 2023)
Computational study on antibody evolution and design
(Seminar at LiMe, Kyoto University 2022)
Molecular modeling in antibody drug discovery
(Symposium on academic drug discovery at Osaka Metropolitan University 2022)
Computer-aided optimization and generation of antibodies
(The 22nd Annual Meeting of the Protein Science Society of Japan 2022)

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Education (2)：

2006 - 2011 Osaka University Institute for Protein Research
2002 - 2006 Kitasato University School of Pharmacy

Professional career (1)：

Ph.D. (Osaka University)

Work history (13)：

2022/04 - 現在 National Institute of Infectious Diseases Laboratory of Vaccine Design, Research Center for Drug and Vaccine Development Senior Scientist
2022/04 - 2023/03 The University of Tokyo College of Arts and Sciences Part-time lecturer
2019/04 - 2022/03 The University of Tokyo Medical Device Development and Regulation Research Center, School of Engineering Lecturer
2018/04 - 2022/03 Chuo University Graduate School of Science and Engineering Part-time lecturer
2018/02 - 2019/03 The University of Tokyo Medical Device Development and Regulation Research Center, School of Engineering Assistant Professor

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Committee career (3)：

2019 - 現在 Rosetta Consortium Rosetta affiliate
2017/01 - 2019/12 The Biophysical Society of Japan Expert committee member (Antibody engineering)
2019 - The Division of Structure-Activity Studies, The Pharmaceutical Society of Japan Executive committee, The Symposium of Structure-Activity Relationships

Awards (3)：

2019 - Japanese Biochemical Society JB Award
2015/11 - The Pharmaceutical Society of Japan Award for Excellent Presentation
2008/06 - Protein Science Society of Japan Best Poster Award

Association Membership(s) (13)：

CHEM-BIO INFORMATICS SOCIETY , JAPANESE SOCIETY FOR BIOINFORMATICS , Japanese Society of Cell Synthesis Research , THE JAPANESE SOCIETY FOR ARTIFICIAL INTELLIGENCE , The Protein Society , THE BIOPHYSICAL SOCIETY OF JAPAN , PROTEIN SCIENCE SOCIETY OF JAPAN , The Association for Natural Language Processing , The Japan Society of Drug Delivery System , The Japanese Society for Vaccinology , Japanese Society for Immunology , THE MOLECULAR SIMULATION SOCIETY OF JAPAN , THE PHARMACEUTICAL SOCIETY OF JAPAN

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