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.


  • 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, S. H., Kawabata, S., Shirai, H., & Mizuguchi, K. 2012 Computational design, construction, and characterization of a set of specificity determining residues in protein–protein interactions. Proteins: Structure, Function, and Bioinformatics 80(10), 2426–2436 doi


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