Kuroda Daisuke 黒田大祐

Researcher Number	60756732
Other IDs	https://orcid.org/0000-0003-2390-4785
Affiliation (Current)	2025: 日本大学, 文理学部, 准教授 2025: 国立健康危機管理研究機構, 国立感染症研究所ワクチン開発研究センター, 主任研究員
Affiliation (based on the past Project Information) *help	2026: 日本大学, 文理学部, 准教授 2024: 国立感染症研究所, 治療薬・ワクチン開発研究センター, 主任研究官 2022: 国立感染症研究所, 治療薬・ワクチン開発研究センター, 主任研究官 2019 – 2022: 東京大学, 大学院工学系研究科(工学部), 講師 2017 – 2018: 東京大学, 大学院工学系研究科(工学部), 助教 2015 – 2016: 昭和大学, 薬学部, 助教
Review Section/Research Field	Principal Investigator Basic Section 62010:Life, health and medical informatics-related / Medium-sized Section 62:Applied informatics and related fields / Life / Health / Medical informatics / Biophysics Except Principal Investigator Basic Section 27040:Biofunction and bioprocess engineering-related / Basic Section 50020:Tumor diagnostics and therapeutics-related / Basic Section 37010:Bio-related chemistry
Keywords	Principal Investigator 機械学習 / 分子設計 / 分子シミュレーション / 抗体設計 / シミュレーション / 抗体 / 凝集性 / 熱安定性 / タンパク質工学 / 抗体工学 … More / データベース / 蛋白質工学 / 感染症 / 中枢神経系 / 脳内輸送 / 計算科学 / 情報技術 / 薬物脳内輸送 / DDS / Supercharging / 単ドメイン抗体 / 分子デザイン / 機能計測 / 物性計測 / ペプチド / 安定性 / 親和性成熟 / ペプチド設計 / 物理化学測定 / 計算化学 / 生命情報科学 / 特異性 / 構造予測 / バイオインフォマティクス … More Except Principal Investigator 蛋白質エンジニアリング / 物理化学 / ダイナミクス / 分子動力学計算 / 金属イオン / CDR / フラクチュエーション / ペプチド / 計算科学 / 受容体 / 抗原 / 抗体 / ネオ抗原 / T細胞受容体 / ネオアンチゲン / 腫瘍浸潤T細胞 / 蛋白質-蛋白質間相互作用 / 蛋白質-蛋白質相互作用 / 低分子 / 相互作用 / リガンド / 速度論 / 熱力学 / 蛋白質 Less

B細胞レパトアから学ぶ抗体の進化と多変数最適化戦略Principal Investigator
- Principal Investigator
  
  黒田大祐
- Project Period (FY)
  2026 – 2029
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  Nihon University
Transporting drugs across the blood-brain barrier through information technologyPrincipal Investigator
- Principal Investigator
  
  Kuroda Daisuke
- Project Period (FY)
  2021 – 2024
- Research Category
  
  Grant-in-Aid for Challenging Research (Pioneering)
- Review Section
  
  Medium-sized Section 62:Applied informatics and related fields
- Research Institution
  National Institute of Infectious Diseases
  The University of Tokyo
Elucidation and Control of Local Fractions in Protein Engineering
- Principal Investigator
  
  Tsumoto Kouhei
- Project Period (FY)
  2020 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 27040:Biofunction and bioprocess engineering-related
- Research Institution
  The University of Tokyo
Comprehensive analysis of cancer-specific antigens recognized by tumor-infiltrating T cells
- Principal Investigator
  
  KIYOTANI Kazuma
- Project Period (FY)
  2019 – 2021
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 50020:Tumor diagnostics and therapeutics-related
- Research Institution
  Japanese Foundation for Cancer Research
Molecular design of real proteins in virtual spacePrincipal Investigator
- Principal Investigator
  
  Kuroda Daisuke
- Project Period (FY)
  2019 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 62010:Life, health and medical informatics-related
- Research Institution
  National Institute of Infectious Diseases
  The University of Tokyo
Elucidation of the weak interaction-triggered system of proteins and its design proposal
- Principal Investigator
  
  NAGATOISHI Satoru
- Project Period (FY)
  2018 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 37010:Bio-related chemistry
- Research Institution
  The University of Tokyo
Engineering antibody stability using molecular simulations and machine learningPrincipal Investigator
- Principal Investigator
  
  Kuroda Daisuke
- Project Period (FY)
  2017 – 2019
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Life / Health / Medical informatics
- Research Institution
  The University of Tokyo
Development of antibody modeling methods toward rational antibody designPrincipal Investigator
- Principal Investigator
  
  Kuroda Daisuke
- Project Period (FY)
  2015 – 2016
- Research Category
  
  Grant-in-Aid for Research Activity Start-up
- Research Field
  
  Biophysics
- Research Institution
  Showa University

All 2023 2022 2021 2020 2019 2018 2017 2016

All Journal Article Presentation Book

[Book] Computer-Aided Antibody Design2022
- Author(s)
  津本浩平、黒田大祐
- Total Pages
  505
- Publisher
  Humana / Springer-Nature
- ISBN
  1071626086
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] 抗体および抗原の分子デザイン計算2023
- Author(s)
  黒田大祐
- Journal Title
  
  理論化学会誌「フロンティア」
  
  Volume: 5(1) Pages: 2-11
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] An Engineered Synthetic Receptor－Aptamer Pair for an Artificial Signal Transduction System2023
- Author(s)
  Hanrui Liu, Toni A. Baeumler, Kai Nakamura, Yuga Okada, Seojung Cho, Akihiro Eguchi, Daisuke Kuroda, Kouhei Tsumoto, Ryosuke Ueki, Shinsuke Sando
- Journal Title
  
  ACS Nano
  
  Volume: in press Issue: 10 Pages: 9039-9048
- DOI
  10.1021/acsnano.2c11744
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint2022
- Author(s)
  Kim J, Kobayashi H, Yokomine M, Shiratori Y, Ueda T, Takeuchi K, Umezawa K, Kuroda D, Tsumoto K, Morimoto J, Sando S.
- Journal Title
  
  Org. Biomol. Chem.
  
  Volume: 20 Issue: 35 Pages: 6994-7000
- DOI
  10.1039/d2ob01300b
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-21H05509, KAKENHI-PROJECT-20H02531, KAKENHI-PROJECT-20H03375, KAKENHI-PROJECT-20H03378, KAKENHI-PROJECT-19H04202
[Journal Article] Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites2022
- Author(s)
  Yokomine Marin、Morimoto Jumpei、Fukuda Yasuhiro、Shiratori Yota、Kuroda Daisuke、Ueda Takumi、Takeuchi Koh、Tsumoto Kouhei、Sando Shinsuke
- Journal Title
  
  Angewandte Chemie International Edition
  
  Volume: 61 Issue: 14 Pages: 6994-7000
- DOI
  10.1002/anie.202200119
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20K21494, KAKENHI-PROJECT-19H03522, KAKENHI-PUBLICLY-21H05509, KAKENHI-PROJECT-20H03375, KAKENHI-PROJECT-20H03378, KAKENHI-PROJECT-19H04202
[Journal Article] 計算化学による抗体の立体構造モデリング2022
- Author(s)
  黒田大祐
- Journal Title
  
  SAR News
  
  Volume: 43 Issue: 0 Pages: 9-23
- DOI
  10.14894/sarnews.43.0_9
- ISSN
  2436-9152
- Year and Date
  2022-10-01
- Language
  Japanese
- Open Access
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics2022
- Author(s)
  Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR.
- Journal Title
  
  mAbs
  
  Volume: 14 Issue: 1 Pages: 2020082-2020082
- DOI
  10.1080/19420862.2021.2020082
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PROJECT-19H04202
[Journal Article] 抗体コンピュータ設計の現在地2022
- Author(s)
  黒田大祐
- Journal Title
  
  実験医学増刊
  
  Volume: 40(20) Pages: 122-129
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR32022
- Author(s)
  Kinoshita Seisho、Nakakido Makoto、Mori Chinatsu、Kuroda Daisuke、Caaveiro Jose M.M.、Tsumoto Kouhei
- Journal Title
  
  Protein Science
  
  Volume: 31 Issue: 11 Pages: 1-12
- DOI
  10.1002/pro.4450
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-21H05090, KAKENHI-PROJECT-20H02531, KAKENHI-PROJECT-20H03228, KAKENHI-PLANNED-19H05766
[Journal Article] Structural Classification of CDR-H3 in Single-Domain VHH Antibodies2022
- Author(s)
  Kuroda Daisuke、Tsumoto Kouhei
- Journal Title
  
  Methods Mol Biol.
  
  Volume: 2552 Pages: 61-79
- DOI
  10.1007/978-1-0716-2609-2_2
- ISBN
  9781071626085, 9781071626092
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H04202
[Journal Article] Peptoid-based reprogrammable template for cell-permeable inhibitors of protein?protein interactions2021
- Author(s)
  Fukuda Y, Yokomine M, Kuroda D, Tsumoto K, Morimoto J, Sando S.
- Journal Title
  
  Chemical Science
  
  Volume: 12 Issue: 40 Pages: 13292-13300
- DOI
  10.1039/d1sc01560e
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PROJECT-19H04202
[Journal Article] Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion2021
- Author(s)
  Senoo Akinobu、Ito Sho、Nagatoishi Satoru、Saito Yutaro、Ueno Go、Kuroda Daisuke、Yoshida Kouhei、Tashima Takumi、Kudo Shota、Sando Shinsuke、Tsumoto Kouhei
- Journal Title
  
  Communications Biology
  
  Volume: 4 Issue: 1 Pages: 1041-1041
- DOI
  10.1038/s42003-021-02575-3
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-18H05425, KAKENHI-PROJECT-19H03522, KAKENHI-PLANNED-19H05766
[Journal Article] Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range2021
- Author(s)
  Kasahara Keisuke、Kuroda Daisuke、Tanabe Aki、Kawade Raiji、Nagatoishi Satoru、Tsumoto Kouhei
- Journal Title
  
  Biochemical and Biophysical Research Communications
  
  Volume: 563 Pages: 54-59
- DOI
  10.1016/j.bbrc.2021.05.053
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-18H05425, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H04202, KAKENHI-PROJECT-20K16377
[Journal Article] Mechanism of dimerization and structural features of human LI-cadherin2021
- Author(s)
  Yui Anna、Caaveiro Jose M.M.、Kuroda Daisuke、Nakakido Makoto、Nagatoishi Satoru、Goda Shuichiro、Maruno Takahiro、Uchiyama Susumu、Tsumoto Kouhei
- Journal Title
  
  Journal of Biological Chemistry
  
  Volume: 297 Issue: 3 Pages: 101054-101054
- DOI
  10.1016/j.jbc.2021.101054
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-18H05425, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766
[Journal Article] Structural basis for antigen recognition by methylated lysine?specific antibodies2021
- Author(s)
  Ishii M, Nakakido M, Caaveiro JMM, Kuroda D, Okumura CJ, Maruyama T, Entzminger K, Tsumoto K.
- Journal Title
  
  Journal of Biological Chemistry
  
  Volume: 296 Pages: 100176-100176
- DOI
  10.1074/jbc.ra120.015996
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-17H06109, KAKENHI-PROJECT-19H04202
[Journal Article] Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors2021
- Author(s)
  Yoshimura Chihoko、Nagatoishi Satoru、Kuroda Daisuke、Kodama Yasuo、Uno Takao、Kitade Makoto、Chong-Takata Khoontee、Oshiumi Hiromi、Muraoka Hiromi、Yamashita Satoshi、Kawai Yuichi、Ohkubo Shuichi、Tsumoto Kouhei
- Journal Title
  
  Journal of Medicinal Chemistry
  
  Volume: 64 Issue: 5 Pages: 2669-2677
- DOI
  10.1021/acs.jmedchem.0c01715
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-18H05425, KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H04202
[Journal Article] Microsecond molecular dynamics suggest that a non-synonymous mutation, frequently observed in patients with mild symptoms in Tokyo, alters dynamics of the SARS-CoV-2 main protease2021
- Author(s)
  Kuroda D, Tsumoto K.
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 18 Issue: 0 Pages: 215-222
- DOI
  10.2142/biophysico.bppb-v18.022
- NAID
  130008088919
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H04202
[Journal Article] Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies2021
- Author(s)
  Ikeuchi E, Kuroda D, Nakakido M, Murakami A, Tsumoto K.
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 20624-20624
- DOI
  10.1038/s41598-021-98977-8
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-17H06109, KAKENHI-PROJECT-19H04202
[Journal Article] Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks2020
- Author(s)
  Koehler Leman J, Weitzner D, Lewis SM, and about 100 others including Kuroda D
- Journal Title
  
  Nature Methods
  
  Volume: 17 Issue: 7 Pages: 665-680
- DOI
  10.1038/s41592-020-0848-2
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H04202
[Journal Article] Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design2020
- Author(s)
  Kuroda Daisuke、Tsumoto Kouhei
- Journal Title
  
  Journal of Pharmaceutical Sciences
  
  Volume: 109 Issue: 5 Pages: 1631-1651
- DOI
  10.1016/j.xphs.2020.01.011
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H04202, KAKENHI-PROJECT-19H03522
[Journal Article] Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions2020
- Author(s)
  Jumpei Morimoto, Jungyeon Kim, Daisuke Kuroda, Satoru Nagatoishi, Kouhei Tsumoto, Shinsuke Sando
- Journal Title
  
  Journal of the American Chemical Society
  
  Volume: 142 Issue: 5 Pages: 2277-2284
- DOI
  10.1021/jacs.9b10496
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K15692, KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-19H04202
[Journal Article] A Peptoid with Ectended Shape in Water2019
- Author(s)
  Morimoto J, Fukuda Y, Kuroda D, Watanabe T, Yoshida F, Asada M, Nakamura T, Senoo A, Nagatoishi S, Tsumoto K, *Sando S
- Journal Title
  
  J Am Chem Soc.
  
  Volume: 141 Issue: 37 Pages: 14612-14623
- DOI
  10.1021/jacs.9b04371
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-19H04202
[Journal Article] Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG162019
- Author(s)
  Kondo Hiroko X.、Kiribayashi Ryo、Kuroda Daisuke、Kohda Jiro、Kugimiya Akimitsu、Nakano Yasuhisa、Tsumoto Kouhei、Takano Yu
- Journal Title
  
  Scientific Reports
  
  Volume: 9 Issue: 1 Pages: 19840-19840
- DOI
  10.1038/s41598-019-56154-y
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K06589, KAKENHI-WRAPUP-19H05451, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-19H04202, KAKENHI-PROJECT-17H06109
[Journal Article] An epitope‐directed antibody affinity maturation system utilizing mammalian cell survival as readout2019
- Author(s)
  Eguchi Akihiro、Nakakido Makoto、Nagatoishi Satoru、Kuroda Daisuke、Tsumoto Kouhei、Nagamune Teruyuki、Kawahara Masahiro
- Journal Title
  
  Biotechnology and Bioengineering
  
  Volume: 116 Issue: 7 Pages: 1742-1751
- DOI
  10.1002/bit.26965
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H01792, KAKENHI-PROJECT-17K19007, KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-17H06109
[Journal Article] Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations.2019
- Author(s)
  Yoshida K, Kuroda D, Kiyoshi M, Nakakido M, Nagatoishi S, Soga S, Shirai H, Tsumoto K.
- Journal Title
  
  Sci Rep.
  
  Volume: 9(1) Issue: 1 Pages: 4482-4482
- DOI
  10.1038/s41598-019-40461-5
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H02420, KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-17H06109
[Journal Article] How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations2019
- Author(s)
  Kawade Raiji、Kuroda Daisuke、Tsumoto Kouhei
- Journal Title
  
  FEBS Letters
  
  Volume: 594 Issue: 5 Pages: 903-912
- DOI
  10.1002/1873-3468.13674
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-19H05766, KAKENHI-PROJECT-19H03522, KAKENHI-PROJECT-19H04202, KAKENHI-PROJECT-19J14494
[Journal Article] Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium.2019
- Author(s)
  Yoshida K, Nagatoishi S, Kuroda D, Suzuki N, Murata T, Tsumoto K.
- Journal Title
  
  Biochemistry
  
  Volume: 58(6) Issue: 6 Pages: 504-508
- DOI
  10.1021/acs.biochem.8b01194
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H02420, KAKENHI-PROJECT-18H02082, KAKENHI-PROJECT-16H04710
[Journal Article] Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification2018
- Author(s)
  Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ
- Journal Title
  
  Frontiers in Immunology
  
  Volume: 9:413 Pages: 1-17
- DOI
  10.3389/fimmu.2018.00413
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113, KAKENHI-PROJECT-16H02420
[Journal Article] Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column2018
- Author(s)
  Kiyoshi M, Caaveiro JMM, Tada M, Tamura H, Tanaka T, Terao Y, Morante K, Harazono A, Hashii N, Shibata H, Kuroda D, Nagatoishi S, Oe S, Ide T, Tsumoto K, Ishii-Watabe A
- Journal Title
  
  Scientific Reports
  
  Volume: 8:3955 Issue: 1 Pages: 1-11
- DOI
  10.1038/s41598-018-22199-8
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113, KAKENHI-PROJECT-16H02420, KAKENHI-PROJECT-15K06962
[Journal Article] Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody2018
- Author(s)
  Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K
- Journal Title
  
  Journal of Biochemistry
  
  Volume: in press
- NAID
  40021625331
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K18113
[Journal Article] Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition.2018
- Author(s)
  Takahashi T, Nagatoishi S, Kuroda D, Tsumoto K.
- Journal Title
  
  PLoS One
  
  Volume: 13(10) Issue: 10 Pages: e0204856-e0204856
- DOI
  10.1371/journal.pone.0204856
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-16H02420, KAKENHI-PROJECT-18H02082
[Journal Article] Structures of the prefusion form of measles virus fusion protein in complex with inhibitors2018
- Author(s)
  Hashiguchi T, Fukuda Y, Matsuoka R, Kuroda D, Kubota M, Shirogane Y, Watanabe S, Tsumoto K, Kohda D, Plemper RK, Yanagi Y
- Journal Title
  
  Proceedings of the National Academy of Sciences of the United States of America
  
  Volume: 115(10) Issue: 10 Pages: 2496-2501
- DOI
  10.1073/pnas.1718957115
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113, KAKENHI-PROJECT-16H02420
[Journal Article] Design and Synthesis of Potent and Highly Selective Orexin 1 Receptor Antagonists with a Morphinan Skeleton and Their Pharmacologies2017
- Author(s)
  Nagase H and Yanagisawa M et al.
- Journal Title
  
  J Med Chem
  
  Volume: 60 Issue: 3 Pages: 1018-1040
- DOI
  10.1021/acs.jmedchem.6b01418
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-ORGANIZER-15H05935, KAKENHI-PROJECT-26220207, KAKENHI-PROJECT-16H05098, KAKENHI-PROJECT-15H06606, KAKENHI-PROJECT-15K19195, KAKENHI-PROJECT-15K16557
[Journal Article] Modeling and docking antibody structures with Rosetta2017
- Author(s)
  Weitzner BD, Jeliazkov J, Lyskov S, Marze NA, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ
- Journal Title
  
  Nature Protocols
  
  Volume: 12 Issue: 2 Pages: 401-416
- DOI
  10.1038/nprot.2016.180
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H06606
[Journal Article] Pushing the backbone in protein-protein docking2016
- Author(s)
  Kuroda D, Gray JJ
- Journal Title
  
  Structure
  
  Volume: 24 Issue: 10 Pages: 1821-1829
- DOI
  10.1016/j.str.2016.06.025
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H06606
[Journal Article] Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking2016
- Author(s)
  Kuroda D, Gray JJ
- Journal Title
  
  Bioinformatics
  
  Volume: in press Issue: 16 Pages: 2451-2456
- DOI
  10.1093/bioinformatics/btw197
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] AlphaFold時代の抗体分子設計2023
- Author(s)
  黒田大祐
- Organizer
  日本化学会春季年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] FcγRIIIa受容体の固定化系と溶液系における抗体認識機構の解明2022
- Author(s)
  長門石曉、木下清晶, 黒田大祐, 小菅啓史, 木吉真人, 石井明子, 寺尾陽介, 井出輝彦, 津本浩平
- Organizer
  第16回バイオ関連化学シンポジウム
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 抗体設計に関する分子シミュレーション研究2022
- Author(s)
  黒田大祐
- Organizer
  スーパーコンピュータワークショップ2021「生体分子の構造・機能・デザインの計算科学」
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] In silico design of cross-reactive antibodies binding to SARS-CoV and SARS-CoV-2 spike RBDs2022
- Author(s)
  安田佳生、黒田大祐、佐々木慈英、中木戸誠、松長遼、橋口隆生、津本浩平
- Organizer
  第60回　日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 足場蛋白質を活用した特定のエピトープ領域に対する抗体取得2022
- Author(s)
  住川　太一、中木戸誠、黒田大祐、津本浩平
- Organizer
  日本化学会生体機能関連化学会若手の会第33回サマースクール
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 情報技術を用いた抗体の進化と分子設計に関する研究2022
- Author(s)
  黒田大祐
- Organizer
  京都大学医生物学研究所ウイルス学の潮流セミナー
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] 表面電荷改変抗体のコロイド安定性・結合親和性とその溶媒依存性の解析2022
- Author(s)
  笠原慶亮、黒田大祐、長門石曉、津本浩平
- Organizer
  第60回　日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 計算・情報技術を用いた抗体設計2022
- Author(s)
  黒田大祐
- Organizer
  第22回日本蛋白質科学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Molecular Basis of Contribution of Intramolecular Interactions between Complementarity Determining Region 3 (CDR3) and Framework Region on Biophysical Properties in Camelid Single-Domain Antibody2022
- Author(s)
  Kinoshita S, Nakakido M, Kuroda D, Jose M. M. Caaveiro, Tsumoto K
- Organizer
  The 36th Annual Symposium of The Protein Society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 抗体創薬における計算・情報科学2022
- Author(s)
  黒田大祐
- Organizer
  第5回大阪公立大学アカデミア創薬シンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Computational design reveals residues in CDR-L3 responsible for maintaining affinity of an anti-measles antibody to Hemagglutinin2022
- Author(s)
  Rimpa Paul, Keisuke Kasahara, Jiei Sasaki, Jorge Fernandez, Ryo Matsunaga, Takao Hashiguchi, Daisuke Kuroda, Kouhei Tsumoto
- Organizer
  Antibody Engineering & Therapeutics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K18310
[Presentation] Superchargingデザインは溶媒選択により抗体の物性を制御できる2022
- Author(s)
  笠原慶亮、黒田大祐、河出来時、田部亜季、長門石曉、津本浩平
- Organizer
  第22回　日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Development of Humanized Single-Domain Antibody Synthetic Libraries Based on Physicochemical Analyses2022
- Author(s)
  木下清晶、中木戸誠、黒田大祐、カアベイロホセ、津本浩平
- Organizer
  第21回東京大学生命科学シンポジウム
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] CDR-Graftingによるヒト化VHHの物性機能解析に基づくヒト化VHH人工合成ライブラリ構築2022
- Author(s)
  木下　清晶、中木戸誠、黒田大祐、Jose M.M. Caaveiro、津本浩平
- Organizer
  第22回　日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Exploring designability of antibodies through computational design2021
- Author(s)
  黒田大祐
- Organizer
  大阪大学・蛋白研セミナー
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] 抗体表面への正荷電残基変異導入による抗体のpH非依存的な熱安定性獲得機構2021
- Author(s)
  笠原慶亮、黒田大祐、河出来時、田部亜季、長門石曉、津本浩平
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] How SNPs in LI-cadherin gene increases the risk of cancer metastasis2021
- Author(s)
  Yui A, Kikuchi C, Goda S, Kudo S, Akiba H, Nakakido M, Kuroda D, Nagatoishi S, Arai O, Iwanari H, Hamakubo T, Tsumoto K
- Organizer
  The International Chemical Congress of Pacific Basin Societies 2021
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 膜蛋白質の膜外領域を認識する抗体の取得2021
- Author(s)
  住川太一、中木戸誠、黒田大祐、津本浩平
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] VHHにおけるCDR3-Framework region間分子内相互作用に着目したフレームワーク改変の物理化学的解析2021
- Author(s)
  木下清晶、中木戸誠、黒田大祐、カアベイロホセ、津本浩平
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] The mechanism by which positive supercharging mutations confer pH-independent thermal stability of an antibody2021
- Author(s)
  笠原慶亮・黒田大祐・河出来時・田部亜季・長門石曉・津本浩平
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Computational analysis of antibodies and antibody-antigen interactions2021
- Author(s)
  黒田大祐, 津本浩平
- Organizer
  第19回あわじ感染と免疫国際フォーラム
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] コンピュータ技術を用いた生体分子の解析と設計2021
- Author(s)
  黒田大祐
- Organizer
  次世代医療技術研究会
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] 膜蛋白質Glut1の細胞外領域を認識する抗体取得法の提案2021
- Author(s)
  住川　太一、中木戸誠、黒田大祐、津本浩平
- Organizer
  第94回　日本生化学会大会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] A novel homodimerization mechanism of LI-cadherin2021
- Author(s)
  Yui A, Caaveiro J.M.M, Kuroda D, Nakakido M, Nagatoishi S, Maruno T, Uchiyama S, Tsumoto K
- Organizer
  The Protein Society 35th Annual Symposium
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] VHH抗体の構造特徴を利用したβ-hairpin型ペプチド設計手法の探索2021
- Author(s)
  山本晃一、中木戸誠、黒田大祐、長門石曉、森本淳平、山東信介、津本浩平
- Organizer
  第21回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Physicochemical studies of mutations in framework regions of VHH focusing on intramolecular interactions with CDR32021
- Author(s)
  木下清晶、中木戸誠,、黒田大祐、カアベイロホセ、津本浩平
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Structural analysis of a peptide fragment grafted onto the Adhiron scaffold2020
- Author(s)
  住川太一、中木戸誠、黒田大祐、津本浩平
- Organizer
  第20回　日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 分子動力学シミュレーションを用いたCDR-Graftingによる合成VHHにおける分子挙動の解析2020
- Author(s)
  木下清晶、中木戸誠、黒田大祐、カアベイロホセ、津本浩平
- Organizer
  第58回　日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Application of β-hairpin structure of VHH CDR3 for peptide designs2020
- Author(s)
  山本晃一、中木戸誠、黒田大祐、長門石曉、森本淳平、山東信介、津本浩平
- Organizer
  2020年度医科学研究所G2発表会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] 分子動力学シミュレーションを用いたCDR-Graftingによる合成VHHにおける分子挙動の解析2020
- Author(s)
  木下清晶、中木戸誠、黒田大祐、カアベイロホセ、津本浩平
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] The Molecular Basis of How SNP in LI-cadherin Affected Cancer Metastasis2020
- Author(s)
  由井杏奈、菊池智佳、郷田秀一郎、工藤翔太、秋葉宏樹、中木戸誠、黒田大祐、長門石曉、新井修、岩成宏子、浜窪隆雄、津本浩平
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] 蛋白質-蛋白質間相互作用の速度論的制御に基づくP-カドヘリンの細胞接着形成阻害2020
- Author(s)
  妹尾暁暢、長門石曉、黒田大祐、伊藤翔、上野剛、齋藤雄太朗、吉田浩平、田島卓実、工藤翔太、山東信介、津本浩平
- Organizer
  第14回　バイオ関連化学シンポジウム
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 計算デザイン Supercharging 抗体の物性機能解析2020
- Author(s)
  笠原慶亮、黒田大祐、河出来時、田部亜季、長門石曉、津本浩平
- Organizer
  第48回構造活性相関シンポジウム
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] The Molecular Basis of How SNP in LI-cadherin Affected Cancer Metastasis2020
- Author(s)
  由井杏奈、菊池智佳、郷田秀一郎、工藤翔太、秋葉宏樹、中木戸誠、黒田大祐、長門石曉、新井修、岩成宏子、浜窪隆雄、津本浩平
- Organizer
  第20回　日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 計算デザイン Supercharging 抗体の物性機能解析2020
- Author(s)
  笠原慶亮、黒田大祐、河出来時、田部亜季、長門石曉、津本浩平
- Organizer
  第48回　構造活性相関シンポジウム
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] VHH抗体β-hairpin型CDR3を利用したペプチド設計手法の探索2020
- Author(s)
  山本晃一、中木戸誠、黒田大祐、長門石曉、森本淳平、山東信介、津本浩平
- Organizer
  第43回日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Molecular basis of increased risk of colorectal cancer metastasis caused by SNPs in LI-cadherin2020
- Author(s)
  由井杏奈、菊池智佳、郷田秀一郎、丸野孝浩、内山進、中木戸誠、黒田大祐、長門石曉、新井修、岩成宏子、浜窪隆雄、津本浩平
- Organizer
  第58回　日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] 蛋白質-蛋白質間相互作用の速度論的制御に基づくP-カドヘリンの細胞接着形成阻害2020
- Author(s)
  妹尾暁暢、長門石曉、黒田大祐、伊藤翔、上野剛、齋藤雄太朗、吉田浩平、田島卓実、工藤翔太、山東信介、津本浩平
- Organizer
  第14回バイオ関連化学シンポジウム
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Molecular basis of increased risk of colorectal cancer metastasis caused by SNPs in LI-cadherin2020
- Author(s)
  由井杏奈、菊池智佳、郷田秀一郎、丸野孝浩、内山進、中木戸誠、黒田大祐、長門石曉、新井修、岩成宏子、浜窪隆雄、津本浩平
- Organizer
  第58回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] VHH抗体β-hairpin型CDR3を利用したペプチド設計手法の探索2020
- Author(s)
  山本晃一、中木戸誠、黒田大祐、長門石曉、森本淳平、山東信介、津本浩平
- Organizer
  第43回　日本分子生物学会年会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] Structural analysis of a peptide fragment grafted onto the Adhiron scaffold2020
- Author(s)
  住川太一、中木戸誠、黒田大祐、津本浩平
- Organizer
  第20回日本蛋白質科学会年会
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Application of β-hairpin structure of VHH CDR3 for peptide designs2020
- Author(s)
  山本晃一、中木戸誠、黒田大祐、長門石曉、森本淳平、山東信介、津本浩平
- Organizer
  2020年度　医科学研究所G2発表会
- Data Source
  KAKENHI-PROJECT-20H02531
[Presentation] がん転移に関するLI-cadherin一塩基多型の分子メカニズム2019
- Author(s)
  由井　杏奈、菊池　智佳、郷田　秀一郎、工藤　翔太、秋葉　宏樹、中木戸　誠、黒田　大祐、長門石　曉、新井　修、岩成　宏子、浜窪　隆雄、津本　浩平
- Organizer
  第92回　日本生化学会大会
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] コンピュータ技術に基づく抗体の物性・機能予測の現状と課題2019
- Author(s)
  黒田大祐
- Organizer
  CBI学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Computational modeling algorithm in antibody engineering: How precise are they?2019
- Author(s)
  黒田大祐, 津本浩平
- Organizer
  19回日本蛋白質科学会年会,
- Invited
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] hermodynamic, kinetic and computational analyses of the recognition mechanism of an antibody to a flexible protein antigen2019
- Author(s)
  金田　生穂、長門石　曉、黒田　大祐、中木戸　誠、カアベイロ　ホセ、津本　浩平
- Organizer
  CBI学会2019年大会
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] Molecular mechanism of how SNP in LI-cadherin affected cancer metastasis2019
- Author(s)
  由井　杏奈、菊池　智佳、郷田　秀一郎、工藤　翔太、秋葉　宏樹、中木戸　誠、黒田　大祐、長門石　曉、新井　修、岩成　宏子、浜窪　隆雄、津本　浩平
- Organizer
  G2 Plus Retreat
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] Addressing the Benefits of Simulations in Computer-aided Antibody Engineering2019
- Author(s)
  Daisuke Kuroda
- Organizer
  Biologics Manufacturing Japan
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19H04202
[Presentation] Analysis of the denaturation midpoint to design the VHH with high thermal stability2018
- Author(s)
  Emina Ikeuchi, Daisuke Kuroda, Makoto Nakakido, Maiko Yoshida, Narutoshi Tsukahara, Akikazu Murakami, Kouhei Tsumoto
- Organizer
  62nd Annual Meeting of the Biophysical Society
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] Structural, physicochemical and computational analysis to reveal the mechanism of recognition of phosphorylated antigen by an antibody2018
- Author(s)
  KAWADE, Raiji; AKIBA, Hiroki; NAKAKIDO, Makoto; KURODA, Daisuke; MARUYAMA, Toshiaki; OKUMURA, Shigeru; ENTZMINGER, Kevin; CAAVEIRO, Jose; TSUMOTO, Kouhei
- Organizer
  日本化学会第98春季年会
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] FcRカラムを用いた異なる細胞種由来IgGの糖鎖解析2018
- Author(s)
  小菅啓史、長門石曉, 中木戸誠, 黒田大祐, 木吉真人, 石井明子, 寺尾陽介, 朝岡義晴, 大江正剛, 井出輝彦, 津本浩平
- Organizer
  第91回日本生化学会大会
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] Nanodisc-GPCRを用いた物理化学的アプローチによる低分子薬剤探索2018
- Author(s)
  吉田浩平、長門石曉、黒田大祐、津本浩平
- Organizer
  第9回スクリーニング学研究会
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] コンピュータ技術を用いたタンパク質のモデリング計算とその応用2018
- Author(s)
  黒田大祐
- Organizer
  東京大学工学部化学生命工学講演会
- Invited
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] Nanodisc を用いたリン脂質二重膜環境中におけるヒトセロトニン受容体の機能解析2018
- Author(s)
  吉田浩平、黒田大祐、長門石曉、津本浩平
- Organizer
  第56回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-18H02082
[Presentation] 分子シミュレーションと物理化学解析による抗体の熱安定性に関する研究2018
- Author(s)
  河上恵理, 黒田大祐、中木戸誠、津本浩平
- Organizer
  日本化学会第98春季年会
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] 分子動力学シミュレーションによる抗HIV中和抗体PG16のCDR-H3の変異における構造への影響2018
- Author(s)
  桐林遼, 近藤寛子, 黒田大祐, 齋藤徹, 香田次郎, 釘宮章光, 中野靖久, 津本浩平, 鷹野優
- Organizer
  第5回生命分子科学研究会
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] Molecular dynamics study of the structural stability of CDR-H3 of anti-HIV neutralizing antibody PG162017
- Author(s)
  Ryo Kiribayashi, Hiroko X. Kondo, Daisuke Kuroda, Toru Saito, Jiro Kohda, Akimitsu Kugimiya1, Yasuhisa Nakano, Yu Takano
- Organizer
  The 57th Sanibel Symposium
- Place of Presentation
  米国フロリダ
- Year and Date
  2017-02-19
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] 抗原配列の硫酸化が抗体との相互作用に与える影響の熱力学的解析2017
- Author(s)
  宮鍋一紘、秋葉宏樹、カアベイロホセ、黒田大祐、中木戸誠、高松祐一郎、山下雄史、津本浩平
- Organizer
  第11回バイオ関連化学シンポジウム
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] アミノ酸電荷交換に関する抗原-抗体相互作用の物理化学解析2017
- Author(s)
  吉田浩平, 木吉真人、黒田大祐、中木戸誠、長門石曉、曽我真司、白井宏樹、津本浩平
- Organizer
  第45回構造活性相関シンポジウム
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] MDシミュレーションによる抗HIV中和抗体PG16のCDR-H3における構造揺らぎの解析2017
- Author(s)
  桐林遼、藤寛子、黒田大祐、齋藤徹、香田次郎、釘宮章光、中野靖久、鷹野優
- Organizer
  日本化学会第97回春季年会
- Place of Presentation
  慶応大学日吉キャンパス
- Year and Date
  2017-03-16
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] Physicochemical analysis of antigen-antibody interaction associated with charge exchange of amino acids, Kouhei Yoshida, Masato Kiyoshi2017
- Author(s)
  Kouhei Yoshida, Masato Kiyoshi, Daisuke Kuroda, Makoto Nakakido, Satoru Nagatoishi, Shinji Soga, Hiroki Shirai, Kouhei Tsumoto
- Organizer
  The Second International Symposium on Biofunctional Chemistry
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] Thermodynamic analysis of the mechanism of peptide recognition by an anti-peptide antibody2017
- Author(s)
  Kazuhiro Miyanabe, Hiroki Akiba, Jose Caaveiro, Daisuke Kuroda, Kouhei Kuroda
- Organizer
  日本化学会第97春季年会
- Place of Presentation
  慶応大学日吉キャンパス
- Year and Date
  2017-03-16
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] Molecular dynamics study of mutation effects on the neutralizing ability in CDR-H3 of an anti-HIV antibody PG162017
- Author(s)
  Ryo Kiribayashi,Hiroko X. Kondo, Daisuke Kuroda, Toru Saito, Jiro Kohda, Akimitsu Kugimiya, Yasuhisa Nakano, Yu Takano
- Organizer
  Swedish-Japanese Workshop on Nano-Structure Science by Novel Light Sources
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] MD法による抗HIV抗体PG16のCDR-H3の変異における中和能への影響の解析2017
- Author(s)
  桐林遼, 近藤寛子, 黒田大祐, 齋藤徹, 香田次郎, 釘宮章光, 中野靖久, 鷹野優
- Organizer
  日本化学会中国四国支部大会鳥取大会
- Data Source
  KAKENHI-PROJECT-17K18113
[Presentation] Energy-based analysis and prediction of peptide-HLA interactions2016
- Author(s)
  黒田大祐、合田浩明
- Organizer
  第44回構造活性相関シンポジウム
- Place of Presentation
  京都大学
- Year and Date
  2016-11-16
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] Molecular dynamics study of the structural rigidity of CDR-H3 of anti-HIV neutralizing antibody PG162016
- Author(s)
  桐林遼、藤寛子、黒田大祐、齋藤徹、香田次郎、釘宮章光、中野靖久、鷹野優
- Organizer
  第54回日本生物物理学会年会
- Place of Presentation
  つくば国際会議場
- Year and Date
  2016-11-25
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] On the shape complementarities of adaptive immune systems to pathogens2016
- Author(s)
  黒田大祐, 合田浩明
- Organizer
  日本蛋白質科学会
- Place of Presentation
  福岡
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] How well can we model peptide-HLA interactions using sequence information alone?2016
- Author(s)
  黒田大祐, 合田浩明
- Organizer
  日本薬学会
- Place of Presentation
  横浜
- Year and Date
  2016-03-26
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] 分子動力学シミュレーションによる抗HIV中和抗体PG16のCDR-H3における構造安定性の解析2016
- Author(s)
  桐林遼、藤寛子、黒田大祐、香田次郎、釘宮章光、中野靖久、鷹野優
- Organizer
  第16回蛋白質科学会年会
- Place of Presentation
  福岡国際会議場
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] 抗ペプチド抗体による抗原ペプチド構造の認識機構の解明2016
- Author(s)
  宮鍋一紘、秋葉宏樹、カアベイロホセ、黒田大祐、中木戸誠、新井修、岩成宏子、浜窪隆雄、津本浩平
- Organizer
  第16回蛋白質科学会年会
- Place of Presentation
  福岡国際会議場
- Year and Date
  2016-06-07
- Data Source
  KAKENHI-PROJECT-15H06606
[Presentation] Molecular dynamics study of the structural rigidity of CDR-H3 of anti-HIV neutralizing antibody PG162016
- Author(s)
  桐林遼、藤寛子、黒田大祐、齋藤徹、香田次郎、釘宮章光、中野靖久、鷹野優
- Organizer
  2016年日本化学会中国四国支部大会　香川大会
- Place of Presentation
  香川大学幸町キャンパス
- Year and Date
  2016-11-05
- Data Source
  KAKENHI-PROJECT-15H06606

1. NAGATOISHI Satoru (30550248)

# of Collaborated Projects: 2 results

# of Collaborated Products: 27 results
2. KIYOTANI Kazuma (30433642)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
3. Tsumoto Kouhei (90271866)

# of Collaborated Projects: 1 results

# of Collaborated Products: 30 results
4. 田部亜季 (60786367)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
5. 森本淳平 (70754935)

# of Collaborated Projects: 1 results

# of Collaborated Products: 3 results
6. 中木戸誠 (80784511)

# of Collaborated Projects: 1 results

# of Collaborated Products: 19 results
7. 安楽泰孝 (60581585)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 橋口隆生 (50632098)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
9. NAGASE Hiroshi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. 上田卓見

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 竹内恒

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 鷹野優

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 近藤寛子

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 河原正浩

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Kuroda Daisuke 黒田 大祐

Research Projects

Research Products

Co-Researchers

B細胞レパトアから学ぶ抗体の進化と多変数最適化戦略Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Transporting drugs across the blood-brain barrier through information technologyPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Elucidation and Control of Local Fractions in Protein Engineering

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Comprehensive analysis of cancer-specific antigens recognized by tumor-infiltrating T cells

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Molecular design of real proteins in virtual spacePrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Elucidation of the weak interaction-triggered system of proteins and its design proposal

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Engineering antibody stability using molecular simulations and machine learningPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

Development of antibody modeling methods toward rational antibody designPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Research Field

Research Institution

[Book] Computer-Aided Antibody Design2022

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] 抗体および抗原の分子デザイン計算2023

Author(s)

Journal Title

Data Source

[Journal Article] An Engineered Synthetic Receptor－Aptamer Pair for an Artificial Signal Transduction System2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] 計算化学による抗体の立体構造モデリング2022

Author(s)

Journal Title

Kuroda Daisuke 黒田大祐