Daisuke Kuroda

5th year Doctor Candidate
(5-year intensive Ph. D. program)

Current Research

• Understanding the sequence-structure relationships in antibodies
• Understanding the relationships between antibody structure and antigen-recognitions

To that end...
• Structural classification and sequence analysis of antibodies by knowledge-based approaches
• Modeling and simulations of loops in antibodies by energy-based approaches
• Implementation of immunological database and annotation in antibody modeling

Publications (^*Corresponding author)

• In silico antibody engineering: Toward high resolution modeling and designs
  
  • Kuroda D^*, Shirai H, Jacobson MP, Nakamura H.

• Use of amino acid composition to predict epitope residues of individual antibodies
  
  • Soga S, Kuroda D, Shirai H, Kobori M, Hirayama N.^*
  • Protein Engineering, Design, and Selections (2010, 23(6):441-8) [Pubmed]

• Systematic classification of CDR-L3 in antibodies: Implicatoins of the light chain sub-types and the V_L-V_H interface
  
  • Kuroda D^*, Shirai H, Kobori M, Nakamura H.
  • PROTEINS: Structure, Function, and Bioinformatics (2009, 75(1):139-146) [Pubmed]

• Structural classification of CDR-H3 revisited: A lesson in antibody modeling
  
  • Kuroda D^*, Shirai H, Kobori M, Nakamura H.
  • PROTEINS: Structure, Function, and Bioinformatics (2008, 73(3):608-620) [Pubmed]

• Protein bioinformatics for drug discovery = concavity druggability and antibody druggability =
  
  • Shirai H^*, Mizuguchi K, Kuroda D, Nakamura H, Soga S, Kobori M, Hirayama N.
  • In: Computational Biology: New Research (2008, pp.11-18) [Nova Publishers]

• H3-rules, progress report 2007
  • Kuroda D, Shirai H, Kobori M, Nakamura H.
  • Journal of Proteomics & Bioinformatics, special issue; Proceedings of PRICPS-AOHUPO 2008 (2008, Vol. 2.2:189-190) [OMICS Publicaions]

• リレー紹介: 日本のバイオインフォマティクス研究室 (中村 春木研究室)
  • 黒田 大祐
  • JSBi News letter, Vol.18 (p.15) 2009

Presentations

Interests

• Computational biology and its experimental validations
  • Immune systems
  • Structural biology
  • Protein engineering
    • Background figure represents TCR and MHC class I proteins, PDB code: 2CKB

Academic Societies

• The Protein Society (USA)
• Biophysical Society of Japan
• Protein Science Society of Japan
• Chem-Bio Informatics Society
• Japanese Society for Bioinformatics

Activities

• Staff (2009), ISCB Student Council Japan Division (生命情報科学若手の会)
• Organizer (2009), The 28th Study Meeting on Theory of Protein and Nucleic Acid Structure (構造理論勉強会)

Awards and Grants

• JSPS Excellent Young Researcher Oversea Visit Program (Jan. 2010 - Aug. 2010)
• Research fellowship of Japan Society for the Promotion of Science (DC2 : Apr. 2009 - Mar. 2011)
• Best Poster Award in the 8th Annual Meeting of the Protein Science Society of Japan (2008)

Contact Information

Kuroda, Daisuke (黒田 大祐)
E-mail: