Biomolecule Analysis Team

Research Topics

Analysis of protein-protein interactions

Various aspects of protein-protein interaction (PPI) have been investigated by combining different types of molecular information. New methods to predict PPI and the interface for PPI have been developed in the studies.

Analysis of enzyme structures and functions

Enzyme structures and functions, including enzyme reaction mechanisms, have been analyzed and classified, in order to develop the enzyme reaction database, EzCatDB, as well as the enzyme-related softwares. Along with enzymes, enzyme-related biomolecules have also been analyzed.


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Team Member

Hiroyuki Toh
Deputy Director Leader E-mail
Hiroyuki Toh
Key Words

protein, amino acid sequence, nucleotide sequence, tertiary structure, protein-protein interaction, homology, molecular evolution


Nozomi Nagano
Senior
Research
Scientist
E-mail
Key Words

Enzyme, Catalytic mechanism, Catalysis, Protein, 3D-structure, Tertiary structure, Catalytic function, Classification database, Ligand, Compound, Intermediate analyses, EzCatDB

Tomoshi Kameda
Senior Research Scientist
E-mail
Key Words

molecular dynamics, replica exchange method, protein folding, amyloid and aggregation


Takatsugu Hirokawa

Additional post
E-mail
Key Words

protein modeling, in silico screening, drug design, molecular simulation, G protein-coupled receptors

Chie Motono

Additional post
E-mail
Key Words

molecular dynamics protein stability, folding, tertiary structure prediction


Papers List

  • Nemoto, W. Toh, H.:"Functional region prediction with a set of appropriate homologous sequences - an index for sequence selection by integrating structure and sequence information with spatial statistics" BMC Struct Biol (in press)
  • Daiyasu, H. Hirokawa, T., Kamiya, N., Toh, H.:"Computational Analysis of Ligand Recognition Mechanisms by Prostaglandin E2 (subtype 2) and D2Receptors" Theor. Chem. Acc. 130, 1131-1143 (2011).
  • Kato T, Nagano N: "Discriminative structural approaches for enzyme active-site prediction." BMC Bioinformatics 12, S49, (2011).
  • Kato T, Nagano N:"Metric learning for enzyme active-site search." Bioinformatics. 26(21):2698-2704 (2010).
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