National Institutes of Biomedical Innovation, Health and Nutrition
Institute for Protein Research

Enzyme structures and functions

  • Analysis and developing prediction methods of specificity of protein-protein, protein-compound interactions
1. Analysis of enzyme detailed functions
  • We showed the subsequences determined by only the literature information and ligand-enzyme complex structures had sufficient information to detect functional subclasses.


  1. Nagao C, Nagano N, Mizuguchi K. Relationships between functional subclasses and information contained in active-site and ligand-binding residues in diverse superfamilies. Proteins 2010;78(10):2369-2384.


Nozomi Nagano (CBRC

2. Analysis of specificity determining residues in protein-protein interactions
  • We defined a “structure-based specificity determining position (sbSDP)” as a set of equivalent residues in a protein family showing a large variation in their interaction energy with different partners. The importance of many sbSDP for determining specificity had been verified experimentally.


  1. Nagao C, Izako N, Soga S, Khan SH, Kawabata S, Shirai H, Mizuguchi K. Computational design, construction and characterization of a set of specificity determining residues in protein-protein interactions., Proteins, 2012, PubMed