The University of Tokyo · Medicine
Professor Daisuke Kuroda's research lab specializes in computational biology and biomaterials science, with a strong focus on antibody drug development and the design of advanced biomaterials for medical applications. The lab pioneers computer-aided methods for modeling antibody structures—particularly the highly variable CDR-H3 region—enabling more accurate prediction of antigen recognition and accelerating therapeutic antibody discovery. In parallel, the lab investigates corrosion-resistant, nickel-free high nitrogen stainless steels for use as implantable biomaterials, evaluating their stability and biocompatibility in physiological environments. These interdisciplinary efforts bridge structural bioinformatics, computational immunology, and materials engineering to advance personalized medicine and implantable device technologies.
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Recent clinical trials using antibodies with low toxicity and high efficiency have raised expectations for the development of next-generation protein therapeutics. However, the process of obtaining therapeutic antibodies remains time consuming and empirical. This review summarizes recent progresses in the field of computer-aided antibody development mainly focusing on antibody modeling, which is divided essentially into two parts: (i) modeling the antigen-binding site, also called the complement
Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the "H3-rules," which classify CDR-H3 stru
Supplementary data are available at Bioinformatics online.
The corrosion resistance of the nickel-free high nitrogen austenitic stainless steel without manganese, Fe–23Cr–2Mo–1.5N (mass%) (HNS) as biomaterials, was evaluated by the polarization test in various electrolytes: 0.9%NaCl solution (saline), phosphate buffered saline (PBS(-)), Hanks’ solution (Hanks) and Eagle’s minimum essential medium (E-MEM). Conventional austenitic stainless steel, 316L, was also polarized for comparison. The both alloys were spontaneously passivated in all electrolytes. T
Antibody modeling is widely used for the analysis of antibody-antigen interactions and for the design of potent antibody drugs. The antibody combining site is composed of six complementarity determining regions (CDRs). The CDRs, except for CDR-H3, which is the most diverse CDR, form limited numbers of canonical structures, which can be identified from the amino acid sequences. A method to classify the CDR-H3 structure from its amino acid sequence was previously proposed. However, since those CDR
Ingots of ferritic stainless steels, Fe–24Cr and Fe–24Cr–2Mo in mass%, were worked to various dimensions for test specimens. Nitrogen was absorbed by the specimens in a furnace filled with nitrogen gas with a pressure of 101.3 kPa at 1473 K to develop a simple and convenient manufacturing process of nickel-free austenitic stainless steels. Changes in the mechanical properties of the alloys with nitrogen absorption treatment are discussed on the basis of the resultant microstructure. Ferritic Fe–
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