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Kuroda Daisuke  黒田 大祐

Researcher Number 60756732
Other IDs
  • ORCIDhttps://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 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
Medium-sized Section 62:Applied informatics and related fields / Basic Section 62010:Life, health and medical informatics-related / 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 / 分子シミュレーション / 抗体設計 / シミュレーション / 凝集性 / 熱安定性 / タンパク質工学 / 分子設計 / 抗体工学 / データベース … More / 蛋白質工学 / 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 / 抗体 / 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
  • Research Projects

    (7 results)
  • Research Products

    (88 results)
  • Co-Researchers

    (14 People)
  •  Transporting drugs across the blood-brain barrier through information technologyPrincipal Investigator

    • Principal Investigator
      黒田 大祐
    • 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
      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
  •  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
  •  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
  •  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 2022 2021 2020 2019 2018 2017 2016

All Journal Article Presentation

  • [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
  • [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] 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] 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
    • Data Source
      KAKENHI-PROJECT-20H02531, KAKENHI-PLANNED-19H05766
  • [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
  • [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
  • [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
  • [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] 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] 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] 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] 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] 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] 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] 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] 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] 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] 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: 1 results
  • 5.  森本 淳平 (70754935)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 1 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
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  • 8.  橋口 隆生 (50632098)
    # of Collaborated Projects: 1 results
    # of Collaborated Products: 0 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

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