RESEARCH
I use both theoretical and experimental methods to study the architecture and function of proteins. I am also involved in protein structure determination by X-ray crystallography. My favorite proteins are ones involved in immune systems, such as antibody, TCR and HLA, and viral proteins. Currently, my interests are twofold: 1) de novo design of immunological proteins and 2) prediction of neoantigen.


PUBLICATIONS

Peer-reviwed papers (Equally contribution, *Corresponding Author)

2017
  1. TBA 
    Jeliazkov et al. (in preparation, 2017)

  2. TBA 
    Miyanabe et al. (submitted, 2017)

  3. TBA 
    Kiyoshi et al. (submitted, 2017)

  4. TBA 
    Hashiguchi et al. (submitted, 2017)

  5. Design and Synthesis of Potent and Highly Selective Orexin 1 Receptor Antagonists with a Morphinan Skeleton and their Pharmacologies 
    Nagase H*, Yamamoto N, Yata M, Ohrui S, Okada T, Saitoh T, Kutsumura N, Nagumo Y, Irukayama-Tomobe Y, Ishikawa Y, Ogawa Y, Hirayama S, Kuroda D, Watanabe Y, Gouda H, and Yanagisawa M.
    Journal of Medicinal Chemistry (2017, 60(3):1018-1040) [Pubmed] [Online]
  1. Modeling and docking antibody structures with Rosetta 
    Weitzner BD, Jeliazkov J, Lyskov S, Marze NA, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, and Gray JJ.
    Nature Protocols (2017, 12(2):401-416) [Pubmed] [Online] [bioRxiv]
2016
  1. Pushing the backbone in protein-protein docking 
    Kuroda D and Gray JJ*.
    Structure (2016, 24(10):1821-1829) [Pubmed] [Online]
  1. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking
    Kuroda D and Gray JJ*.
    Bioinformatics (2016, 32(16):2451-6) [Pubmed] [Online]
  1. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment
    Lensink MF*, Velankar S, Kryshtafovych A and about 99 others including Marze N, Kuroda D, Roy Burman S, and Gray JJ.
    Proteins: Structure, Function, and Bioinformatics  (2016, S1:323-48) [Pubmed] [Online]
  1. Large-Scale Sequence and Structural Comparisons of Human Naïve and Antigen-Experienced Antibody Repertoires 
    DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, and Georgiou GG*.
    Proc. Natl. Acad. Sci. USA (2016, 113(19):E2636-45) [Pubmed] [Online]
2015
  1. Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase
    Kusakabe Y, Ishihara M, Umeda T, Kuroda D, Nakanishi M, Kitade Y, Gouda H, Nakamura KT, and Tanaka N*.
    Scientific Reports (2015, 5:16641) [Pubmed] [Online]
  1. Design and Synthesis of Non-Peptide, Selective Orexin Receptor 2 Agonists
    Nagahara T, Saitoh T, Kutsumura N, Irukayama-Tomobe Y, Ogawa Y, Kuroda D, Gouda H, Kumagai H, Fujii H, Yanagisawa M, and Nagase H*.
    Journal of Medicinal Chemistry (2015, 58(20): 7931-7) [Pubmed] [Online]
2014
  1. Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization
    Weitzner BD, Kuroda D, Marze N, Xu J, and Gray JJ*.
    Proteins: Structure, Function, and Bioinformatics  (2014, 82(8): 1611-23) [Pubmed] [Online]
2013
  1. Extending RosettaDock with water, sugar and pH for prediction of complex structures and affinities for CAPRI rounds 20-27
    Kilambi KP, Pacella M, Xu J, Labonte J, Porter J, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, and Gray JJ*.
    Proteins: Structure, Function, and Bioinformatics  (2013, 81(12): 2201-9) [Pubmed] [Online]
  1. Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)
    Lyskov S, Chou FC, Conchúir SO, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ*, and Das R*.
    PLOS ONE (2013, 8(5):e63906) [Pubmed] [Online]
2012
  1. Computer-aided antibody design
    Kuroda D*, Shirai H, Jacobson MP, and Nakamura H.
    Protein Engineering, Design, and Selection (2012, 25(10):507-22) [Pubmed] [Online]
2011
  1. Bridging the gap between single-template and fragment based protein structure modeling using Spanner
    Lis M†, Kim T†, Sarmiento JJ, Kuroda D, Dinh HV, Kinjo AR, Amada K, Devadas S, Nakamura H*, and Standley DM*.
    Immunome Research (2011, 7(1):1-8) [Online]
2010
  1. Use of amino acid composition to predict epitope residues of individual antibodies
    Soga S, Kuroda D, Shirai H, Kobori M, and Hirayama N*. 
    Protein Engineering, Design, and Selection (2010, 23(6):441-8) [Pubmed] [Online]
2009
  1. Systematic classification of CDR-L3 in antibodies: Implicatoins of the light chain sub-types and the VL-Vinterface
    Kuroda D*, Shirai H, Kobori M, and Nakamura H.
    Proteins: Structure, Function, and Bioinformatics (2009, 75(1):139-46) [Pubmed] [Online]
2008
  1. Structural classification of CDR-H3 revisited: A lesson in antibody modeling
    Kuroda D*, Shirai H, Kobori M, and Nakamura H.
    Proteins: Structure, Function, and Bioinformatics (2008, 73(3):608-20) [Pubmed] [Online]

Non-peer reviewed books (Chapters)
  1. Antibody Informatics
    Shirai H and Kuroda D.
    In: Frontier of Antibody Engineering for Next-generation Therapeutics (次世代医薬開発に向けた抗体工学の最前線, 2012, Chapter 4.1, pp.27-46) [CMC Publishing Co., Ltd.] In Japanese
  1. Protein bioinformatics for drug discovery = concavity druggability and antibody druggability =
    Shirai H, Mizuguchi K, Kuroda D, Nakamura H, Soga S, Kobori M, and Hirayama N.
    In: Computational Biology: New Research (2008, pp.11-18) [Nova Publishers]

Proceedings
  1. Structural classification and modeling of antibody hypervariable loops: knowledge-based approaches
    Kuroda D, Shirai H, Lis M, Kinjo AR, Standley DM, and Nakamura H.
    Protein Science, special issue: The 23rd Symposium of The Protein Society, Boston, Massachusetts, July 24-29, 2009 (2009, Vol.18(S1):144) [Wiley]
  1. H3-rules, progress report 2007
    Kuroda D, Shirai H, Kobori M, and Nakamura H.
    Journal of Proteomics & Bioinformatics, special issue: Proceedings of PRICPS-AOHUPO 2008 (2008, Vol. 2.2:189-190) [Online]

Misc (in Japanese)


Ph.D. THESIS
  • Antibody Structure Analysis and Prediction for Computational Design
    Kuroda D., Osaka University, 2011 (黒田 大祐, 大阪大学 生命機能研究科, 2011年3月).