Ph.D., Osaka University, Mar. 2011

Database

DDS

Structural Biology

Computational science

Antibody

Vaccine

Bioinformatics

Computational Design

Infectious disease

Informatics

Genome Science

Synthetic Biology

Systems Biology

Life sciences, Biophysics

Life sciences, Immunology, Vaccine

Informatics, Biological, health, and medical informatics, Bioinformatics

Life sciences, Systems genomics, Modeling and simulation

Life sciences, Structural biochemistry, Biophysical chemistry

Informatics, Intelligent informatics, Molecular design

Apr. 2025 - Present
Japan Institute for Health Security, Research Center for Vaccine development, National Institute of Infectious Diseases, Visiting Fellow

Apr. 2025 - Present
Nihon University, Department of Biosciences, College of Humanities and Sciences, Associate Professor

Apr. 2022 - Mar. 2025
National Institute of Infectious Diseases, Laboratory of Vaccine Design, Research Center for Drug and Vaccine Development, Senior Scientist

Apr. 2022 - Mar. 2023
The University of Tokyo, College of Arts and Sciences, Part-time lecturer

Apr. 2019 - Mar. 2022
The University of Tokyo, Medical Device Development and Regulation Research Center, School of Engineering, Lecturer

Apr. 2018 - Mar. 2022
Chuo University, Graduate School of Science and Engineering, Part-time lecturer

Feb. 2018 - Mar. 2019
The University of Tokyo, Medical Device Development and Regulation Research Center, School of Engineering, Assistant Professor

Apr. 2017 - Jan. 2018
The University of Tokyo, Department of Bioengineering, School of Engineering, Research Scientist

Apr. 2015 - Mar. 2017
Showa University, School of Pharmacy, Assistant Professor

Oct. 2014 - Mar. 2015
The University of Tokyo, Department of Bioengineering, School of Engineering, Postdoctoral Research Fellow

Oct. 2011 - Sep. 2014
Johns Hopkins University, Department of Chemical & Biomolecular Engineering, Postdoctoral Research Fellow

Apr. 2011 - Sep. 2011
Osaka University, Immunology Frontier Research Center, Postdoctoral Research Fellow

Apr. 2009 - Mar. 2011
JSPS, Research Fellow (DC2)

Nov. 2010 - Dec. 2010
MRC National Institute for Medical Research, Department of Mathematical Biology, Visiting Scholar

Sep. 2009 - Aug. 2010
University of California, San Francisco, Department of Pharmaceutical Chemistry, Jr. Specialist

Apr. 2006 - Mar. 2011
Osaka University, Institute for Protein Research

Apr. 2002 - Mar. 2006
Kitasato University, School of Pharmacy

Oct. 2025 - Present
Editorial committee of PSSJ Archives, Protein Science Society of Japan

2006 - Present

May 2025 - Oct. 2025
Event Committee, The 1st International Online Conference by Antibodies (IOCAB 2025)

Jan. 2017 - Dec. 2019
Expert committee member (Antibody engineering), The Biophysical Society of Japan

2019
Executive committee, The Symposium of Structure-Activity Relationships, The Division of Structure-Activity Studies, The Pharmaceutical Society of Japan

2019
Japanese Biochemical Society, JB Award
★

Nov. 2015
The Pharmaceutical Society of Japan, Award for Excellent Presentation

Jun. 2008
Protein Science Society of Japan, Best Poster Award

★Genetic diversity of pangolin coronaviruses reveals a key immuno-evasive substitution at spike residue 519
Maximilian Stanley Yo; Yu Kaku; Yusuke Kosugi; Jarel Elgin Tolentino; Daisuke Kuroda; Yunlong Richard Cao; Kei Sato
Journal of Virology, May 2026, Refereed, Not invited

★Hybrid Supercharged Antibodies: A Rational Approach to Boost Immunoassay Sensitivity via Controlled Nanoparticle Adsorption
Junichi Sato; Keisuke Kasahara; Satoru Nagatoishi; Keisuke Murakami; Daisuke Kuroda; Jose M. M. Caaveiro; Hirokazu Nagai; Kouhei Tsumoto
Langmuir, Apr. 2026, Refereed, Not invited

★Observation of redistribution for local conformational dynamics in cross-reactive antibody design
Yoshiki Yasuda; Satoru Nagatoishi; Jiei Sasaki; Ryo Matsunaga; Daisuke Kuroda; Takao Hashiguchi; Kouhei Tsumoto
The Journal of Biochemistry, Apr. 2026, Refereed, Not invited
Corresponding

★Intra-patient neuraminidase mutations in avian H5N1 influenza virus reduce sialidase activity to complement weaker hemagglutinin binding and facilitate human infection
Yohei Watanabe; Madiha S. Ibrahim; Yasuha Arai; Daisuke Kuroda; Emad M. Elgendy; Shin-ichi Nakakita; Yohei Takeda; Vuong Nghia Bui; Takao Ono; Shota Ushiba; Tomo Daidoji; Nongluk Sriwilaijaroen; Haruko Ogawa; Kazuhiko Matsumoto; Yasuo Suzuki; Takaaki Nakaya
PLOS Pathogens, Jan. 2026, Refereed, Not invited

★Optimizing the breadth of SARS-CoV-2-neutralizing antibodies in vivo and in silico
Daisuke Kuroda; Saya Moriyama; Hiroaki Sasaki; Yoshimasa Takahashi
Human Vaccines & Immunotherapeutics, Jul. 2025, Refereed, Invited
Lead

Developing FGF2 Mutants with Selectively Reduced Heparan Sulfate Affinity to Explore Their Impact on FGFR1 Signaling
Yuga Okada; Akihiro Eguchi; Daisuke Kuroda; Kouhei Tsumoto; Ryosuke Ueki; Shinsuke Sando
ChemBioChem, Jul. 2025, Refereed, Not invited

Improving the solubility of single domain antibodies using VH‐like hallmark residues
Yuta Uto; Makoto Nakakido; Takanori Yokoo; Jorge Fernandez‐Perez; Kevin Entzminger; Toshiaki Maruyama; C. J. Okumura; Daisuke Kuroda; Jose M. M. Caaveiro; Kouhei Tsumoto
Protein Science, Jun. 2025, Refereed, Not invited

Development of a small compound that regulates the function of a maltodextrin-binding protein of Streptococcus pyogenes by multifaceted screenings
Tsukushi Yamawaki; Makoto Nakakido; Satoru Nagatoishi; Jose M. M. Caaveiro; Daisuke Kuroda; Chihiro Aikawa; Ichiro Nakagawa; Kouhei Tsumoto
Scientific Reports, Jun. 2025, Refereed, Not invited

Supercharging design of an anti-lysozyme Fab antibody to regulate ligand-dependent reversible aggregation
Keisuke Kasahara; Makoto Nakakido; Daisuke Kuroda; Satoru Nagatoishi; Kouhei Tsumoto
Polymer Journal, Apr. 2025, Refereed, Invited

Affinity-stability trade-off mechanism of residue 35 in framework region 2 of VHH antibodies with β-hairpin CDR3.
Koichi Yamamoto; Satoru Nagatoishi; Ryo Matsunaga; Makoto Nakakido; Daisuke Kuroda; Kouhei Tsumoto
Protein science, Apr. 2025, Refereed, Not invited

Molecular convergence of neutralizing antibodies in human revealed by repeated rabies vaccination
Mizuki Fujisawa; Taishi Onodera; Daisuke Kuroda; Chidchamai Kewcharoenwong; Michihito Sasaki; Yukari Itakura; Kohei Yumoto; Arnone Nithichanon; Naoto Ito; Shinji Takeoka; Tadaki Suzuki; Hirofumi Sawa; Ganjana Lertmemongkolchai; Yoshimasa Takahashi
npj Vaccines, Feb. 2025, Refereed, Not invited
Corresponding

Unveiling the structural mechanisms behind high affinity and selectivity in phosphorylated epitope-specific rabbit antibodies
Keisuke Kasahara; Raiji Kawade; Makoto Nakakido; Ryo Matsunaga; Hiroki Akiba; Kevin C. Entzminger; Toshiaki Maruyama; Shigeru C.J. Okumura; Jose M.M. Caaveiro; Daisuke Kuroda; Kouhei Tsumoto
Journal of Biological Chemistry, Nov. 2024, Refereed, Not invited
Corresponding

Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Hisano Yajima; Yuki Anraku; Yu Kaku; Kanako Terakado Kimura; Arnon Plianchaisuk; Kaho Okumura; Yoshiko Nakada-Nakura; Yusuke Atarashi; Takuya Hemmi; Daisuke Kuroda; Yoshimasa Takahashi; Shunsuke Kita; Jiei Sasaki; Hiromi Sumita; Keita Matsuno; Naganori Nao; Hirofumi Sawa; Keita Mizuma; Jingshu Li; Izumi Kida; Yume Mimura; Yuma Ohari; Shinya Tanaka; Masumi Tsuda; Lei Wang; Yoshikata Oda; Zannatul Ferdous; Kenji Shishido; Hiromi Mohri; Miki Iida; Takasuke Fukuhara; Tomokazu Tamura; Rigel Suzuki; Saori Suzuki; Shuhei Tsujino; Hayato Ito; Naoko Misawa; Ziyi Guo; Alfredo A. Hinay; Kaoru Usui; Wilaiporn Saikruang; Spyridon Lytras; Keiya Uriu; Ryo Yoshimura; Shusuke Kawakubo; Luca Nishumura; Yusuke Kosugi; Shigeru Fujita; Jarel Elgin M.Tolentino; Luo Chen; Lin Pan; Wenye Li; Maximilian Stanley Yo; Kio Horinaka; Mai Suganami; Mika Chiba; Kyoko Yasuda; Keiko Iida; Adam Patrick Strange; Naomi Ohsumi; Shiho Tanaka; Eiko Ogawa; Tsuki Fukuda; Rina Osujo; Kazuhisa Yoshimura; Kenji Sadamas; Mami Nagashima; Hiroyuki Asakura; Isao Yoshida; So Nakagawa; Kazuo Takayama; Rina Hashimoto; Sayaka Deguchi; Yukio Watanabe; Yoshitaka Nakata; Hiroki Futatsusako; Ayaka Sakamoto; Naoko Yasuhara; Tateki Suzuki; Yukari Nakajima; Takashi Irie; Ryoko Kawabata; Kaori Sasaki-Tabata; Terumasa Ikeda; Hesham Nasser; Ryo Shimizu; M. S. T. Monira Begum; Michael Jonathan; Yuka Mugita; Sharee Leong; Otowa Takahashi; Takamasa Ueno; Chihiro Motozono; Mako Toyoda; Akatsuki Saito; Anon Kosaka; Miki Kawano; Natsumi Matsubara; Tomoko Nishiuchi; Jiri Zahradnik; Prokopios Andrikopoulos; Miguel Padilla-Blanco; Aditi Konar; Jumpei Ito; Katsumi Maenaka; Kei Sato; Takao Hashiguchi
Nature Communications, Oct. 2024, Refereed, Not invited

Triphenylphosphonium-modified catiomers enhance in vivo mRNA delivery through stabilized polyion complexation
Jumpei Norimatsu; Hayato L. Mizuno; Takayoshi Watanabe; Takumi Obara; Makoto Nakakido; Kouhei Tsumoto; Horacio Cabral; Daisuke Kuroda; Yasutaka Anraku
Materials Horizons, Jul. 2024, Refereed, Not invited
Corresponding

Impact of single-residue mutations on protein thermal stability: The case of threonine 83 of BC2L-CN lectin
Megumi Hoya; Ryo Matsunaga; Satoru Nagatoishi; Teruhiko Ide; Daisuke Kuroda; Kouhei Tsumoto
International Journal of Biological Macromolecules, Jun. 2024, Refereed, Not invited

Functional insights of Tyr37 in framework region 2 directly contributing to the binding affinities and dissociation kinetics in single-domain VHH antibodies
Koichi Yamamoto; Satoru Nagatoishi; Makoto Nakakido; Daisuke Kuroda; Kouhei Tsumoto
Biochemical and Biophysical Research Communications, May 2024, Refereed, Not invited

Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes
Akinobu Senoo; Masato Hoshino; Toshiki Shiomi; Makoto Nakakido; Satoru Nagatoishi; Daisuke Kuroda; Ichiro Nakagawa; Jeremy R. H. Tame; Jose M. M. Caaveiro; Kouhei Tsumoto
Scientific Reports, Mar. 2024, Refereed, Not invited

Unveiling the affinity–stability relationship in anti-measles virus antibodies: a computational approach for hotspots prediction
Rimpa Paul; Keisuke Kasahara; Jiei Sasaki; Jorge Fernández Pérez; Ryo Matsunaga; Takao Hashiguchi; Daisuke Kuroda; Kouhei Tsumoto
Frontiers in Molecular Biosciences, Mar. 2024, Refereed, Not invited
Corresponding

Editorial: Progress and challenges in computational structure-based design and development of biologic drugs
Traian Sulea; Sandeep Kumar; Daisuke Kuroda
Frontiers in Molecular Biosciences, Feb. 2024, Refereed, Invited
Last

Generation of antibodies to an extracellular region of the transporters Glut1/Glut4 by immunization with a designed antigen
Taichi Sumikawa; Makoto Nakakido; Ryo Matsunaga; Daisuke Kuroda; Satoru Nagatoishi; Kouhei Tsumoto
Journal of Biological Chemistry, Feb. 2024, Refereed, Not invited

Conformational features and interaction mechanisms of VHH antibodies with β‐hairpin CDR3: A case of Nb8‐HigB2 interaction
Koichi Yamamoto; Satoru Nagatoishi; Ryo Matsunaga; Makoto Nakakido; Daisuke Kuroda; Kouhei Tsumoto
Protein Science, Nov. 2023, Refereed, Not invited

Biophysical insight into protein-protein interactions in the Interleukin-11/Interleukin-11Rα/glycoprotein 130 signaling complex
Chinatsu Mori; Satoru Nagatoishi; Ryo Matsunaga; Daisuke Kuroda; Makoto Nakakido; Kouhei Tsumoto
Biochemical and Biophysical Research Communications, Nov. 2023, Refereed, Not invited

Targeting hemoglobin receptors IsdH and IsdB of Staphylococcus aureus with a single VHH antibody inhibits bacterial growth
Sandra Valenciano-Bellido; Jose M.M. Caaveiro; Makoto Nakakido; Daisuke Kuroda; Chihiro Aikawa; Ichiro Nakagawa; Kouhei Tsumoto
Journal of Biological Chemistry, Sep. 2023, Refereed, Not invited

Arginine cluster introduction on framework region in anti‐lysozyme antibody improved association rate constant by changing conformational diversity of CDR loops
Shingo Maeta; Makoto Nakakido; Hiroaki Matsuura; Naoki Sakai; Kunio Hirata; Daisuke Kuroda; Atsushi Fukunaga; Kouhei Tsumoto
Protein Science, Aug. 2023, Refereed, Not invited

Modulation of a conformational ensemble by a small molecule that inhibits key protein–protein interactions involved in cell adhesion
Akinobu Senoo; Satoru Nagatoishi; Daisuke Kuroda; Sho Ito; Go Ueno; Jose M. M. Caaveiro; Kouhei Tsumoto
Protein Science, Aug. 2023, Refereed, Not invited

Structural basis for cross-group recognition of an influenza virus hemagglutinin antibody that targets postfusion stabilized epitope
Keisuke Tonouchi; Yu Adachi; Tateki Suzuki; Daisuke Kuroda; Ayae Nishiyama; Kohei Yumoto; Haruko Takeyama; Tadaki Suzuki; Takao Hashiguchi; Yoshimasa Takahashi
PLOS Pathogens, Aug. 2023, Refereed, Not invited

Structural delineation and computational design of SARS-CoV-2-neutralizing antibodies against Omicron subvariants.
Saya Moriyama; Yuki Anraku; Shunta Taminishi; Yu Adachi; Daisuke Kuroda; Shunsuke Kita; Yusuke Higuchi; Yuhei Kirita; Ryutaro Kotaki; Keisuke Tonouchi; Kohei Yumoto; Tateki Suzuki; Taiyou Someya; Hideo Fukuhara; Yudai Kuroda; Tsukasa Yamamoto; Taishi Onodera; Shuetsu Fukushi; Ken Maeda; Fukumi Nakamura-Uchiyama; Takao Hashiguchi; Atsushi Hoshino; Katsumi Maenaka; Yoshimasa Takahashi
Nature Communications, Jul. 2023, Refereed, Not invited

An Engineered Synthetic Receptor-Aptamer Pair for an Artificial Signal Transduction System.
Hanrui Liu; Toni A Baeumler; Kai Nakamura; Yuga Okada; Seojung Cho; Akihiro Eguchi; Daisuke Kuroda; Kouhei Tsumoto; Ryosuke Ueki; Shinsuke Sando
ACS nano, May 2023, Refereed, Not invited

Molecular mechanism underlying the increased risk of colorectal cancer metastasis caused by single nucleotide polymorphisms in LI-cadherin gene.
Anna Yui; Daisuke Kuroda; Takahiro Maruno; Makoto Nakakido; Satoru Nagatoishi; Susumu Uchiyama; Kouhei Tsumoto
Scientific reports, Apr. 2023, Refereed, Not invited

Structural Classification of CDR-H3 in Single-Domain VHH Antibodies.
Daisuke Kuroda; Kouhei Tsumoto
Methods in molecular biology (Clifton, N.J.), 2023, Not refereed, Invited
Lead

ACE2 N-glycosylation modulates interactions with SARS-CoV-2 spike protein in a site-specific manner.
Ayana Isobe; Yasuha Arai; Daisuke Kuroda; Nobuaki Okumura; Takao Ono; Shota Ushiba; Shin-Ichi Nakakita; Tomo Daidoji; Yasuo Suzuki; Takaaki Nakaya; Kazuhiko Matsumoto; Yohei Watanabe
Communications biology, Nov. 2022, Refereed, Not invited
Lead

Molecular basis for thermal stability and affinity in a VHH: Contribution of the framework region and its influence in the conformation of the CDR3
Seisho Kinoshita; Makoto Nakakido; Chinatsu Mori; Daisuke Kuroda; Jose M.M. Caaveiro; Kouhei Tsumoto
Protein Science, Oct. 2022, Refereed, Not invited

Residue-based program of a β-peptoid twisted strand shape via a cyclopentane constraint
Jungyeon Kim; Hiroka Kobayashi; Marin Yokomine; Yota Shiratori; Takumi Ueda; Koh Takeuchi; Koji Umezawa; Daisuke Kuroda; Kouhei Tsumoto; Jumpei Morimoto; Shinsuke Sando
Organic & Biomolecular Chemistry, Sep. 2022, Refereed, Not invited

Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites.
Marin Yokomine; Jumpei Morimoto; Yasuhiro Fukuda; Yota Shiratori; Daisuke Kuroda; Takumi Ueda; Koh Takeuchi; Kouhei Tsumoto; Shinsuke Sando
Angewandte Chemie (International ed. in English), Mar. 2022, Refereed, Not invited

Current advances in biopharmaceutical informatics: Guidelines, impact and challenges in the computational developability assessment of antibody therapeutics
Rahul Khetan; Robin Curtis; Charlotte M. Deane; Johannes Thorling Hadsund; Uddipan Kar; Konrad Krawczyk; Daisuke Kuroda; Sarah A. Robinson; Pietro Sormanni; Kouhei Tsumoto; Jim Warwicker; Andrew C.R. Martin
mAbs, Feb. 2022, Refereed, Not invited

Regulation of cadherin dimerization by chemical fragments as a trigger to inhibit cell adhesion
Akinobu Senoo; Sho Ito; Satoru Nagatoishi; Yutaro Saito; Go Ueno; Daisuke Kuroda; Kouhei Yoshida; Takumi Tashima; Shota Kudo; Shinsuke Sando; Kouhei Tsumoto
Communications Biology, Dec. 2021, Refereed, Not invited

Delicate balance among thermal stability, binding affinity, and conformational space explored by single-domain VHH antibodies.
Emina Ikeuchi; Daisuke Kuroda; Makoto Nakakido; Akikazu Murakami; Kouhei Tsumoto
Scientific reports, Oct. 2021, Refereed, Not invited
Lead

Mechanism of dimerization and structural features of human LI-cadherin
Anna Yui; Jose M.M. Caaveiro; Daisuke Kuroda; Makoto Nakakido; Satoru Nagatoishi; Shuichiro Goda; Takahiro Maruno; Susumu Uchiyama; Kouhei Tsumoto
Journal of Biological Chemistry, Sep. 2021, Refereed, Not invited

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein–protein interactions
Yasuhiro Fukuda; Marin Yokomine; Daisuke Kuroda; Kouhei Tsumoto; Jumpei Morimoto; Shinsuke Sando
Chemical Science, Aug. 2021, Refereed, Not invited

Anion solvation enhanced by positive supercharging mutations preserves thermal stability of an antibody in a wide pH range.
Keisuke Kasahara; Daisuke Kuroda; Aki Tanabe; Raiji Kawade; Satoru Nagatoishi; Kouhei Tsumoto
Biochemical and Biophysical Research Communications, May 2021, Refereed, Not invited
Corresponding

Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors
Chihoko Yoshimura; Satoru Nagatoishi; Daisuke Kuroda; Yasuo Kodama; Takao Uno; Makoto Kitade; Khoontee Chong-Takata; Hiromi Oshiumi; Hiromi Muraoka; Satoshi Yamashita; Yuichi Kawai; Shuichi Ohkubo; Kouhei Tsumoto
Journal of Medicinal Chemistry, Mar. 2021, Refereed, Not invited

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 protease
Daisuke Kuroda; Kouhei Tsumoto
Biophysics and Physicobiology, 2021
Lead

Structural basis for antigen recognition by methylated lysine–specific antibodies
Misaki Ishii; Makoto Nakakido; Jose M.M. Caaveiro; Daisuke Kuroda; C.J. Okumura; Toshiaki Maruyama; Kevin Entzminger; Kouhei Tsumoto
Journal of Biological Chemistry, 2021, Refereed, Not invited

Macromolecular modeling and design in Rosetta: recent methods and frameworks
Julia Koehler Leman; Brian D. Weitzner; Steven M. Lewis; Jared Adolf-Bryfogle; Nawsad Alam; Rebecca F. Alford; Melanie Aprahamian; David Baker; Kyle A. Barlow; Patrick Barth; Benjamin Basanta; Brian J. Bender; Kristin Blacklock; Jaume Bonet; Scott E. Boyken; Phil Bradley; Chris Bystroff; Patrick Conway; Seth Cooper; Bruno E. Correia; Brian Coventry; Rhiju Das; René M. De Jong; Frank DiMaio; Lorna Dsilva; Roland Dunbrack; Alexander S. Ford; Brandon Frenz; Darwin Y. Fu; Caleb Geniesse; Lukasz Goldschmidt; Ragul Gowthaman; Jeffrey J. Gray; Dominik Gront; Sharon Guffy; Scott Horowitz; Po-Ssu Huang; Thomas Huber; Tim M. Jacobs; Jeliazko R. Jeliazkov; David K. Johnson; Kalli Kappel; John Karanicolas; Hamed Khakzad; Karen R. Khar; Sagar D. Khare; Firas Khatib; Alisa Khramushin; Indigo C. King; Robert Kleffner; Brian Koepnick; Tanja Kortemme; Georg Kuenze; Brian Kuhlman; Daisuke Kuroda; Jason W. Labonte; Jason K. Lai; Gideon Lapidoth; Andrew Leaver-Fay; Steffen Lindert; Thomas Linsky; Nir London; Joseph H. Lubin; Sergey Lyskov; Jack Maguire; Lars Malmström; Enrique Marcos; Orly Marcu; Nicholas A. Marze; Jens Meiler; Rocco Moretti; Vikram Khipple Mulligan; Santrupti Nerli; Christoffer Norn; Shane Ó’Conchúir; Noah Ollikainen; Sergey Ovchinnikov; Michael S. Pacella; Xingjie Pan; Hahnbeom Park; Ryan E. Pavlovicz; Manasi Pethe; Brian G. Pierce; Kala Bharath Pilla; Barak Raveh; P. Douglas Renfrew; Shourya S. Roy Burman; Aliza Rubenstein; Marion F. Sauer; Andreas Scheck; William Schief; Ora Schueler-Furman; Yuval Sedan; Alexander M. Sevy; Nikolaos G. Sgourakis; Lei Shi; Justin B. Siegel; Daniel-Adriano Silva; Shannon Smith; Yifan Song; Amelie Stein; Maria Szegedy; Frank D. Teets; Summer B. Thyme; Ray Yu-Ruei Wang; Andrew Watkins; Lior Zimmerman; Richard Bonneau
Nature Methods, Jun. 2020, Refereed, Not invited

Engineering Stability, Viscosity, and Immunogenicity of Antibodies by Computational Design
Daisuke Kuroda; Kouhei Tsumoto
Journal of Pharmaceutical Sciences, May 2020, Refereed, Invited
Lead

How the protonation state of a phosphorylated amino acid governs molecular recognition: insights from classical molecular dynamics simulations
Raiji Kawade; Daisuke Kuroda; Kouhei Tsumoto
FEBS Letters, Mar. 2020, Refereed, Not invited
Corresponding

Per-Residue Program of Multiple Backbone Dihedral Angles of β-Peptoids via Backbone Substitutions
Jumpei Morimoto; Jungyeon Kim; Daisuke Kuroda; Satoru Nagatoishi; Kouhei Tsumoto; Shinsuke Sando
Journal of the American Chemical Society, Feb. 2020, Refereed, Not invited

Exploring designability of electrostatic complementarity at an antigen-antibody interface directed by mutagenesis, biophysical analysis, and molecular dynamics simulations
Kouhei Yoshida; Daisuke Kuroda; Masato Kiyoshi; Makoto Nakakido; Satoru Nagatoishi; Shinji Soga; Hiroki Shirai; Kouhei Tsumoto
Scientific Reports, Dec. 2019, Refereed

Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16
Hiroko X. Kondo; Ryo Kiribayashi; Daisuke Kuroda; Jiro Kohda; Akimitsu Kugimiya; Yasuhisa Nakano; Kouhei Tsumoto; Yu Takano
Scientific Reports, Dec. 2019, Refereed, Not invited
Corresponding

A Peptoid with Extended Shape in Water.
Jumpei Morimoto; Yasuhiro Fukuda; Daisuke Kuroda; Takumu Watanabe; Fumihiko Yoshida; Mizue Asada; Toshikazu Nakamura; Akinobu Senoo; Satoru Nagatoishi; Kouhei Tsumoto; Shinsuke Sando
Journal of the American Chemical Society, Sep. 2019, Refereed, Not invited

An epitope‐directed antibody affinity maturation system utilizing mammalian cell survival as readout
Akihiro Eguchi; Makoto Nakakido; Satoru Nagatoishi; Daisuke Kuroda; Kouhei Tsumoto; Teruyuki Nagamune; Masahiro Kawahara
Biotechnology and Bioengineering, Jul. 2019, Refereed, Not invited

Phospholipid Membrane Fluidity Alters Ligand Binding Activity of a G Protein-Coupled Receptor by Shifting the Conformational Equilibrium.
Kouhei Yoshida; Satoru Nagatoishi; Daisuke Kuroda; Nanao Suzuki; Takeshi Murata; Kouhei Tsumoto
Biochemistry, Feb. 2019, Refereed, Not invited

Thermodynamic and computational analyses reveal the functional roles of the galloyl group of tea catechins in molecular recognition
Tomoya Takahashi; Satoru Nagatoishi; Daisuke Kuroda; Kouhei Tsumoto
PLOS ONE, Oct. 2018, Refereed, Not invited

Antibody Affinity Maturation by Computational Design.
Daisuke Kuroda; Kouhei Tsumoto
Methods in molecular biology (Clifton, N.J.), Sep. 2018, Not refereed, Invited
Lead

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.
Kazuhiro Miyanabe; Hiroki Akiba; Daisuke Kuroda; Makoto Nakakido; Osamu Kusano-Arai; Hiroko Iwanari; Takao Hamakubo; Jose M M Caaveiro; Kouhei Tsumoto
Journal of biochemistry, Jul. 2018, Refereed, Not invited

Structures of the prefusion form of measles virus fusion protein in complex with inhibitors
Takao Hashiguchi; Yoshinari Fukuda; Rei Matsuoka; Daisuke Kuroda; Marie Kubota; Yuta Shirogane; Shumpei Watanabe; Kouhei Tsumoto; Daisuke Kohda; Richard Karl Plemper; Yusuke Yanagi
Proceedings of the National Academy of Sciences, Mar. 2018, Refereed, Not invited

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification
Jeliazko R. Jeliazkov; Adnan Sljoka; Daisuke Kuroda; Nobuyuki Tsuchimura; Naoki Katoh; Kouhei Tsumoto; Jeffrey J. Gray
Frontiers in Immunology, Mar. 2018, Refereed, Not invited

Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column.
Masato Kiyoshi; Jose M M Caaveiro; Minoru Tada; Hiroko Tamura; Toru Tanaka; Yosuke Terao; Koldo Morante; Akira Harazono; Noritaka Hashii; Hiroko Shibata; Daisuke Kuroda; Satoru Nagatoishi; Seigo Oe; Teruhiko Ide; Kouhei Tsumoto; Akiko Ishii-Watabe
Scientific reports, Mar. 2018, Refereed, Not invited

Design and Synthesis of Potent and Highly Selective Orexin 1 Receptor Antagonists with a Morphinan Skeleton and Their Pharmacologies
Hiroshi Nagase; Naoshi Yamamoto; Masahiro Yata; Sayaka Ohrui; Takahiro Okada; Tsuyoshi Saitoh; Noriki Kutsumura; Yasuyuki Nagumo; Yoko Irukayama-Tomobe; Yukiko Ishikawa; Yasuhiro Ogawa; Shigeto Hirayama; Daisuke Kuroda; Yurie Watanabe; Hiroaki Gouda; Masashi Yanagisawa
Journal of Medicinal Chemistry, Feb. 2017, Refereed, Not invited

Modeling and docking of antibody structures with Rosetta
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
Nature Protocols, Feb. 2017, Refereed, Not invited

Pushing the Backbone in Protein-Protein Docking.
Daisuke Kuroda; Jeffrey J Gray
Structure, Oct. 2016, Refereed, Not invited
Lead

Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment
Marc F. Lensink; Sameer Velankar; Andriy Kryshtafovych; Shen‐You Huang; Dina Schneidman‐Duhovny; Andrej Sali; Joan Segura; Narcis Fernandez‐Fuentes; Shruthi Viswanath; Ron Elber; Sergei Grudinin; Petr Popov; Emilie Neveu; Hasup Lee; Minkyung Baek; Sangwoo Park; Lim Heo; Gyu Rie Lee; Chaok Seok; Sanbo Qin; Huan‐Xiang Zhou; David W. Ritchie; Bernard Maigret; Marie‐Dominique Devignes; Anisah Ghoorah; Mieczyslaw Torchala; Raphaël A.G. Chaleil; Paul A. Bates; Efrat Ben‐Zeev; Miriam Eisenstein; Surendra S. Negi; Zhiping Weng; Thom Vreven; Brian G. Pierce; Tyler M. Borrman; Jinchao Yu; Françoise Ochsenbein; Raphaël Guerois; Anna Vangone; João P.G.L.M. Rodrigues; Gydo van Zundert; Mehdi Nellen; Li Xue; Ezgi Karaca; Adrien S.J. Melquiond; Koen Visscher; Panagiotis L. Kastritis; Alexandre M.J.J. Bonvin; Xianjin Xu; Liming Qiu; Chengfei Yan; Jilong Li; Zhiwei Ma; Jianlin Cheng; Xiaoqin Zou; Yang Shen; Lenna X. Peterson; Hyung‐Rae Kim; Amit Roy; Xusi Han; Juan Esquivel‐Rodriguez; Daisuke Kihara; Xiaofeng Yu; Neil J. Bruce; Jonathan C. Fuller; Rebecca C. Wade; Ivan Anishchenko; Petras J. Kundrotas; Ilya A. Vakser; Kenichiro Imai; Kazunori Yamada; Toshiyuki Oda; Tsukasa Nakamura; Kentaro Tomii; Chiara Pallara; Miguel Romero‐Durana; Brian Jiménez‐García; Iain H. Moal; Juan Férnandez‐Recio; Jong Young Joung; Jong Yun Kim; Keehyoung Joo; Jooyoung Lee; Dima Kozakov; Sandor Vajda; Scott Mottarella; David R. Hall; Dmitri Beglov; Artem Mamonov; Bing Xia; Tanggis Bohnuud; Carlos A. Del Carpio; Eichiro Ichiishi; Nicholas Marze; Daisuke Kuroda; Shourya S. Roy Burman; Jeffrey J. Gray; Edrisse Chermak; Luigi Cavallo; Romina Oliva; Andrey Tovchigrechko; Shoshana J. Wodak
Proteins: Structure, Function, and Bioinformatics, Sep. 2016, Refereed, Invited

Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking
Daisuke Kuroda; Jeffrey J. Gray
Bioinformatics, Aug. 2016, Refereed, Not invited
Lead

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires
Brandon J. DeKosky; Oana I. Lungu; Daechan Park; Erik L. Johnson; Wissam Charab; Constantine Chrysostomou; Daisuke Kuroda; Andrew D. Ellington; Gregory C. Ippolito; Jeffrey J. Gray; George Georgiou
Proceedings of the National Academy of Sciences, May 2016, Refereed, Not invited

Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase
Yoshio Kusakabe; Masaaki Ishihara; Tomonobu Umeda; Daisuke Kuroda; Masayuki Nakanishi; Yukio Kitade; Hiroaki Gouda; Kazuo T. Nakamura; Nobutada Tanaka
Scientific Reports, Dec. 2015, Refereed, Not invited

Design and Synthesis of Non-Peptide, Selective Orexin Receptor 2 Agonists
Takashi Nagahara; Tsuyoshi Saitoh; Noriki Kutsumura; Yoko Irukayama-Tomobe; Yasuhiro Ogawa; Daisuke Kuroda; Hiroaki Gouda; Hidetoshi Kumagai; Hideaki Fujii; Masashi Yanagisawa; Hiroshi Nagase
Journal of Medicinal Chemistry, Oct. 2015, Refereed, Not invited

Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization
Brian D. Weitzner; Daisuke Kuroda; Nicholas Marze; Jianqing Xu; Jeffrey J. Gray
Proteins: Structure, Function, and Bioinformatics, Aug. 2014, Refereed, Invited
Lead

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27
Krishna Praneeth Kilambi; Michael S. Pacella; Jianqing Xu; Jason W. Labonte; Justin R. Porter; Pravin Muthu; Kevin Drew; Daisuke Kuroda; Ora Schueler-Furman; Richard Bonneau; Jeffrey J. Gray
Proteins: Structure, Function, and Bioinformatics, Dec. 2013, Refereed, Invited

Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE)
Sergey Lyskov; Fang-Chieh Chou; Shane Ó. Conchúir; Bryan S. Der; Kevin Drew; Daisuke Kuroda; Jianqing Xu; Brian D. Weitzner; P. Douglas Renfrew; Parin Sripakdeevong; Benjamin Borgo; James J. Havranek; Brian Kuhlman; Tanja Kortemme; Richard Bonneau; Jeffrey J. Gray; Rhiju Das
PLoS ONE, May 2013, Refereed, Not invited

Computer-aided antibody design
Daisuke Kuroda; Hiroki Shirai; Matthew P. Jacobson; Haruki Nakamura
Protein Engineering Design and Selection, Oct. 2012, Refereed, Not invited
Lead

Bridging the gap between single-template and fragment based protein structure modeling using Spanner
Mieszko Lis; Taeho Kim; Jamica J. Sarmiento; Daisuke Kuroda; Huy Viet Dinh; Akira R. Kinjo; Karlou Amada; Srinivas Devadas; Haruki Nakamura; Daron M. Standley
Immunome Research, 2011, Refereed, Not invited

Use of amino acid composition to predict epitope residues of individual antibodies
Shinji Soga; Daisuke Kuroda; Hiroki Shirai; Masato Kobori; Noriaki Hirayama
Protein Engineering, Design and Selection, Mar. 2010, Refereed, Not invited

Systematic classification of CDR-L3 in antibodies: Implications of the light chain subtypes and the VL-VH interface
Daisuke Kuroda; Hiroki Shirai; Masato Kobori; Haruki Nakamura
Proteins: Structure, Function, and Bioinformatics, Jan. 2009, Refereed, Not invited
Lead

Structural classification of CDR-H3 revisited: A lesson in antibody modeling
Daisuke Kuroda; Hiroki Shirai; Masato Kobori; Haruki Nakamura
Proteins: Structure, Function, and Bioinformatics, May 2008, Refereed, Not invited
Lead

★Current status of computer-aided immunogen design
Daisuke Kuroda; Yoshimasa Takahashi
BIO Clinica, May 2024, Not refereed, Invited
Lead

★Computer-aided design of antibodies and vaccine immunogens
Daisuke Kuroda
Frontier, Jan. 2023, Refereed, Invited
Lead

★Computer-aided antibody design
Daisuke Kuroda
Experimental Medichine, Dec. 2022, Not refereed, Invited
Lead

★Modeling antibody structure through computational chemistry
Daisuke Kuroda
SAR News, Oct. 2022, Not refereed, Invited
Lead

★Current status of computer-aided antibody design
Daisuke Kuroda; Kouhei Tsumoto
Experimental Medicine, Jul. 2018, Not refereed, Invited
Lead

【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
黒田 大祐; 津本 浩平
医学のあゆみ, Aug. 2021, Not refereed, Invited
Lead

【ウイルス感染症に取り組む生物物理学】ウイルス生物物理学 創薬モダリティへの貢献
前仲 勝実; 福原 秀雄; 橋口 隆生; Caaveiro Jose M.M.; 長門石 曉; 黒田 大祐; 津本 浩平
生物物理, Mar. 2021, Not refereed, Invited

バイオ医薬品の分析のコツ 品質評価のための基礎と応用(第7回) タンパク質の分子間相互作用
津本 浩平; 長門石 曉; 中木戸 誠; 黒田 大祐
PHARM TECH JAPAN, Feb. 2018, Not refereed, Invited

★Biopharmaceutical Informatics: Learning to Discover Developable Biotherapeutics
Sandeep Kumar; Andrew E. Nixon, Contributor, Chapter 6: From Deep Generative Models to Structure-Based Simulations: Computational Approaches for Antibody Design【Daisuke Kuroda】
CRC Press, Jan. 2025
9781032291673

★Computer-Aided Antibody Design (Methods in Molecular Biology, 2552)
Kouhei Tsumoto, Daisuke Kuroda, Joint editor
Humana, Nov. 2022
1071626086

The Perfect Manual Interaction Analysis for Drug Discovery
Kouhei Tsumoto; Katsumi Maenaka, Contributor, 1-19 Antibody Structure Prediction and docking, 2-2 Protein-Protein Docking and Interaction Prediction
Yodosha, Dec. 2021
4758122563

Frontier of Antibody Engineering for Next-generation Therapeutics
Izumi Kumagai, Contributor, Chapter 4.1 Antibody Informatics【Hiroki Shirai, Daisuke Kuroda】, pp.27-46
CMC Publishing CO.,LTD., Dec. 2012, Not refereed
9784781306735

Computational Biology: New Research
Alona S Russe, Contributor, Protein bioinformatics for drug discovery = concavity druggability and antibody druggability =【Shirai H, Mizuguchi K, Kuroda D, Nakamura H, Soga S, Kobori M, Hirayama N】, pp.11-18
Nova Science Publishers, Inc., 2009, Not refereed
9781606920404

★Lessons learned from antibody evolution for computational design
Daisuke Kuroda
Biomolecular design workshop 2025, Dec. 2025, Invited

★B-cell repertoire analysis and antibody design
Daisuke Kuroda
The 4th Meeting of the Antibody Society of Japan, Dec. 2025, Invited

★Computer-aided antibody design: Progress and challenges
Daisuke Kuroda
The 25th Annual Meeting of the Protein Science Society of Japan, Jun. 2025, Invited

Computer-aided antibody design
Daisuke Kuroda
Crossroads of Virology and Mathematical Sciences @ RIKEN iTHEMS, Aug. 2025, Not invited

科研費採択と不採択の体験談
黒田大祐
科研費獲得支援講座（日本大学文理学部）, Jul. 2025, Invited

Molecular Basis for the Rational Design of Virus-Neutralizing Antibodies
Daisuke Kuroda
Kickoff Meeting of the Cooperative Research Program（Joint Usage/Research Center program）of Institute for Life and Medical Sciences, Kyoto University, May 2025, Not invited

Probing Antibody Evolution and Potential Molecular Design Using Computational Methods
Daisuke Kuroda
5th Life Science Seminar at Department of Biosciences, College of Humanities and Sciences, Nihon University, Dec. 2024, Invited

Pursuing Broadly Neutralizing Antibodies for Rational Vaccine Design
Daisuke Kuroda
Computational Vaccinology Symposium, Oct. 2024, Invited

Exploring antibody evolution through computational and physicochemical approaches
Daisuke Kuroda
The 16th Annual Westin Immunogenicity Seminar, Oct. 2024, Invited

Computational Approaches for the Design and Discovery of Broad Neutralizing Antibodies Against SARS-CoV-2
Daisuke Kuroda; Saya Moriyama; Kohei Yumoto; Yu Adachi; Taishi Onodera; Yoshimasa Takahashi
第2回新型コロナウイルス研究集会, Aug. 2024, Not invited

In silico evolution of SARS-CoV-2 antibodies in humans increases the resilience against emerging Omicron subvariants
Daisuke Kuroda; Saya Moriyama; Kohei Yumoto; Yu Adachi; Taishi Onodera; Yoshimasa Takahashi
The 52nd Annual Meeting of the Japanese Society for Immunology, Jan. 2024, Not invited

Computer-aided antibody design in the era of AlphaFold
Daisuke Kuroda
the 103rd CSJ Annual Meeting (2023), Mar. 2023, Invited

Computational study on antibody evolution and design
Daisuke Kuroda
Seminar at LiMe, Kyoto University, Dec. 2022, Invited

Molecular modeling in antibody drug discovery
Daisuke Kuroda
Symposium on academic drug discovery at Osaka Metropolitan University, Sep. 2022, Invited

Computer-aided optimization and generation of antibodies
Daisuke Kuroda
The 22nd Annual Meeting of the Protein Science Society of Japan, Jun. 2022, Invited

Exploring designability of antibodies through molecular simulations
Daisuke Kuroda
Supercomputer Workshop 2021, Jan. 2022, Invited

Computational analysis and design of biomolecules
Daisuke Kuroda
次世代医療技術研究会 令和3年度 第3回情報交換会, Oct. 2021, Invited

Computational analysis of antibodies and antibody-antigen interactions
Daisuke Kuroda, Kouhei Tsumoto
The 19th Awaji International Forum on Infection and Immunity / The Neo-Virology Symposium, Sep. 2021, Invited

Exploring designability of antibodies through computational design
Daisuke Kuroda
IPR Seminar (Antibody engineering with AI towards next generation drug discovery), Aug. 2021, Invited

Computer-aided antibody design: current status and future prospects
Daisuke Kuroda
Focused Session in CBI Anual Meeting 2019, Oct. 2019, Invited

採択者アドバイス
黒田 大祐
科研費 計画調書作成講習会（東京大学大学院工学系研究科）, Sep. 2019, Invited

Addressing the Benefits of Simulations in Computer-aided Antibody Engineering
Daisuke Kuroda
Biologics Manufacturing Japan 2019, Sep. 2019, Invited

Computational modeling algorithms in antibody engineering: How precise are they?
Daisuke Kuroda, Kouhei Tsumoto
Workshop in Joint Annual Meeting of 71st JSCB & 19th PSSJ, Jun. 2019, Invited

Exploring antibody designability through physicochemical analyses, mutagenesis and computations
Daisuke Kuroda
New Frontiers of Protein Design and Engineering: Structure, Function, and Application, IMS Symposium, Mar. 2019, Invited

Protein Informatics
Daisuke Kuroda
Seminar at Sysmex, Dec. 2018, Invited

Computer-aided Antibody Engineering
Daisuke Kuroda
4th Workshop of Protein Engineering at Protein Science Society of Japan, Jun. 2018, Invited

Modeling Protein Structures and Interactions through Computer Simulations
Daisuke Kuroda
Lecture series, The University of Tokyo, Mar. 2018, Invited

コンピュータを用いた蛋白質の研究
Daisuke Kuroda
昭和大学 薬学部 納涼会セミナー, Jul. 2015, Invited

Interplay between conformer selection and induced-fit in protein-protein recognition: Insight from docking simulations
Daisuke Kuroda
先端融合科学シンポジウム 生体分子のダイナミクスを眺める, Jan. 2015, Invited

Five years research life at IPR and the following 4 years
Daisuke Kuroda
IPR Retreat 2014, Dec. 2014, Invited

蛋白質複合体構造予測の現状と課題: フレキシブルドッキング手法開発に向けての取り組み
Daisuke Kuroda
IPR Seminar, Jan. 2014, Invited

Antibody structure prediction toward design
Daisuke Kuroda
IPR Seminar, Jan. 2014, Invited

Capturing Binding-Induced Conformational Changes in Protein Engineering Calculations
Kuroda D; Gray JJ
AIChE 2013 Annual Meeting, Nov. 2013, Not invited

Pushing the Backbone in Flexible Protein-Protein Docking
Kuroda D
RosettaCon 2013, Jul. 2013, Not invited

PDB情報を用いた抗体相補性決定領域の構造分類・予測/MD計算を用いた構造探索
Daisuke Kuroda
The 28th Study Meeting on Theory of Protein and Nucleic Acid Structure, Jul. 2009, Not invited

計算機による抗体設計: 薬らしさの指標の提案
Daisuke Kuroda
1st meeting of ISCB student council Japan Division, Apr. 2009, Not invited

Protein Informatics for antibody drug discovery
Daisuke Kuroda
CIB Seminar, Jan. 2009, Invited

計算機による抗体設計実現に向けて: 知識ベースによるアプローチ
Daisuke Kuroda
Bioinformatics研究若手の会, Oct. 2008, Not invited

データベース解析による蛋白質の配列・構造・機能相関研究
Daisuke Kuroda
The exchange of young researchers in Kobe Univ, Aug. 2008, Not invited

抗体カノニカル構造再訪
Daisuke Kuroda
The 27th Study Meeting on Theory of Protein and Nucleic Acid Structure, Jun. 2008, Not invited

Drug discovery
Sep. 2026 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Introduction to Programing for Biosciences
Sep. 2026 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Bioinformatics 2
Sep. 2025 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Sep. 2025 - Present

Bioinformatics
Sep. 2025 - Present
Graduate School of Integrated Basic Sciences, Nihon University

Structural Biology
Sep. 2025 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Apr. 2025 - Present

Apr. 2025 - Present

Bioinformatics 1
Apr. 2025 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Bioscience Data Processing
Apr. 2025 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Basic Mathematics
Apr. 2025 - Present
Department of Biosciences, College of Humanities and Sciences, Nihon University

Biotechnology
Sep. 2025 - Mar. 2026
Department of Biosciences, College of Humanities and Sciences, Nihon University

Introduction to Programing for Biosciences
Sep. 2025 - Mar. 2026
Department of Biosciences, College of Humanities and Sciences, Nihon University

Biological Sciences
2020 - 2022
The University of Tokyo

Data Science Tutorial
2020 - 2021
School of Engineering, The University of Tokyo

Bioengineering Seminars
2018 - 2021
School of Engineering, The University of Tokyo

Biotechnology II
2018 - 2021
School of Engineering, The University of Tokyo

Experiments and Exercises in Genetic engineering
2018 - 2021
School of Engineering, The University of Tokyo

Basic Biomedical Engineering I
2018 - 2021
Collage of Arts and Science, The University of Tokyo

Basic Medical Biology
2018 - 2021
Graduate School of Science and Engineering, Chuo University

Basics for Functional Chemistry II
2018 - 2021
School of Engineering, The University of Tokyo

Development of Research on Pharmaceutical and Medical Sciences
2015 - 2016
Showa University School of Pharmacy

Advanced Pharmaceutical English
2015 - 2016
Showa University School of Pharmacy

Practice in the Pharmaceutical Curriculum
2015 - 2016
Showa University School of Pharmacy

Research on Pharmaceutical and Medical Sciences
2015 - 2016
Showa University School of Pharmacy

Practical Training for Pharmacy Practice
2015 - 2016
Showa University School of Pharmacy

Early Exposure
2015 - 2016
Showa University School of Pharmacy

Practice in Physical Chemistry and Analytical Chemistry
2015 - 2016
Showa University School of Pharmacy

Interdisciplinary Problem Based Learning Tutorial Ｂ
2015 - 2015
Showa University School of Pharmacy

JAPANESE SOCIETY FOR BIOINFORMATICS

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

Learning Antibody Evolution and Multi-Objective Optimization Strategies from B-Cell Repertoires
Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research, Apr. 2026 - Mar. 2030
Daisuke Kuroda, Kazuma Tomizuka, Masato Kiyoshi

Molecular Foundations for the Theoretical Design of Neutralizing Antibodies Based on Large Language Models
Institute for Life and Medical Sciences, Kyoto University, Cooperative Research Program (Joint Usage/Research Center program), Apr. 2026 - Mar. 2027
Daisuke Kuroda, Takao Hashiguchi

Advancement of Structure-Based B-cell Repertoire Mining Technology and Its Application to Antibody Miniaturization
AMED, Japan Program for Infectious Diseases Research and Infrastructure (Interdisciplinary Cutting-edge Research), Nov. 2024 - Mar. 2027
Daisuke Kuroda; Yoshimasa Takahashi, Adnan Sljoka, Takao Hashiguchi, Satoru Nagatoishi

Evolution of humoral immune memory for resisting viral escape
AMED, Advanced Research and Development Programs for Medical Innovation (AMED-CREST), Oct. 2022 - Mar. 2028
Yoshimasa Takahashi; Kazuo Yamashita; Katsumi Maenaka; Daisuke Kuroda (untill 2025.3)

データ駆動型サイエンスによる中分子細胞膜透過性の創造
JST, CREST, Oct. 2021 - Mar. 2027
Shinsuke Sando; Issei Sato; Koji Umezawa; Daisuke Kuroda (until 2022.3)

Molecular Basis for the Rational Design of Virus-Neutralizing Antibodies
Institute for Life and Medical Sciences, Kyoto University, Cooperative Research Program (Joint Usage/Research Center program), Apr. 2025 - Mar. 2026
Daisuke Kuroda, Takao Hashiguchi

Study of brain organoids and mouse models for the therapeutic application of paramyxovirus central nervous system infection
AMED, Japan Program for Infectious Diseases Research and Infrastructure, Jun. 2023 - Mar. 2026
Takao Hashiguchi, Mototsugu Eiraku, Yasunari Sakai, Daisuke Kuroda, Jumpei Morimoto

Transporting drugs across the blood-brain barrier through information technology
Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Jul. 2021 - Mar. 2025
Daisuke Kuroda; Anraku Yasutaka; Takao Hashiguchi

Development of molecular design and screening method of broadly neutralizing antibodies using structural information
AMED, 新興・再興感染症に対する革新的医薬品等開発推進研究事業, Oct. 2023 - Mar. 2024
Saya Moriyama; Daisuke Kuroda

Development of computing/information platform for analysis of B-cell repertoires associated with infectious diseases
AMED, Japan Program for Infectious Diseases Research and Infrastructure (Interdisciplinary Cutting-edge Research), Dec. 2021 - Mar. 2024
Daisuke Kuroda; Yoshimasa Takahashi, Adnan Sljoka, Takao Hashiguchi, Satoru Nagatoishi

Drug developments based on the study of molecular mechanisms of paramyxovirus infections in the central nervous system
AMED, 新興・再興感染症研究基盤創生事業(多分野融合研究領域), Jul. 2020 - Mar. 2023
Takao Hashiguchi, Yasunari Sakai, Shumpei Watanabe, Daisuke Kuroda

Fine tuning of receptor agonist activity with in silico design
AMED, Research on Development of New Drugs, Jun. 2020 - Mar. 2023
Shinsuke Sando; Ryosuke Ueki; Daisuke Kuroda

蛋白質エンジニアリングにおけるローカルフラクチュエーションの解明とその制御
日本学術振興会, 科学研究費助成事業, Apr. 2020 - Mar. 2023
津本 浩平; 長門石 曉; 黒田 大祐; 中木戸 誠

Molecular design of real proteins in virtual space
Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Apr. 2019 - Mar. 2023
Daisuke Kuroda, Jumpei Morimoto, Aki Tanabe

Development of the system for humanized sigle domain antibodies acquisition based on biophysical and computational approach
AMED, 創薬基盤推進研究事業, May 2018 - Mar. 2023
Makoto Nakakido, Daisuke Kuroda

Development of a drug discovery platform targeting intracellular protein-protein interactions based on peptoid
AMED, 創薬基盤推進研究事業, Dec. 2019 - Mar. 2022
Jumpei Morimoto, Daisuke Kuroda

腫瘍浸潤T細胞が認識するがん特異的抗原の網羅的解析
日本学術振興会, 科学研究費助成事業, Apr. 2019 - Mar. 2022
清谷 一馬; 黒田 大祐

リード創製を指向した物理化学的品質評価技術の開発と支援
AMED, 創薬等ライフサイエンス研究支援基盤事業, Apr. 2017 - Mar. 2022
Kouhei Tsumoto; Satoru Nagatoishi; Makoto Nakakido; Daisuke Kuroda

Rational Antibody Design Through Machine Learning and Moleculer Simulations
The Okawa Foundation for Information and Telecommunications, The Research Grant, Jan. 2021 - Dec. 2021
Daisuke Kuroda

蛋白質の弱い相互作用トリガーシステムの解明とその設計提案
日本学術振興会, 科学研究費助成事業, Apr. 2018 - Mar. 2021
長門石 曉; 黒田 大祐

構造生物学的手法による麻疹ウイルス中枢神経持続感染の治療薬創出を目指した研究
AMED, 感染症研究革新イニシアティブ (J-RRIDE), Aug. 2017 - Mar. 2020
Takao Hashiguchi; Shumpei Watanabe; Daisuke Kuroda

Engineering antibody stability using molecular simulations and machine learning
Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Apr. 2017 - Mar. 2020
Kuroda Daisuke

Development of antibody modeling methods toward rational antibody design
Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Aug. 2015 - Mar. 2017
Kuroda Daisuke

構造バイオインフォマティクスによる抗体抗原認識機構の解明と新規抗体設計手法の開発
日本学術振興会, 科学研究費助成事業 特別研究員奨励費, 2009 - 2010
黒田 大祐

★Rosetta affiliate
Planning etc
Rosetta Consortium, 2019 - Present

Guest Editor (Progress and Challenges in Computational Structure-Based Design and Development of Biologic Drugs)
Planning etc
Frontiers in Molecular Biosciences, 2023

The 28th Study Meeting on Theory of Protein and Nucleic Acid Structure
Planning etc
2009

Japanese Society for Young Bioinformatics Researchers
Planning etc
2009

1st Study Meeting on Bioinformatics for Young Researchers
Planning etc
2008