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Department of Complex Systems Science

KOIKE, Ryotaro
Life-Science Informatics Group
Assistant Professor
Dr. of Science
Research Field
Structural bioinformatics / Biophysics

Current Research

Database analysis of protein structures and functions



Proteins play essential rolls in various biological processes in living bodies. It is my goal to understand the mechanism of the processes comprehensively. There are a great variety of proteins found in cells, and the computational approach is powerful in analyzing them extensively. A protein usually folds into a structure and performs a function. Therefore, information of protein structures are of great benefit to understanding protein functions. The computational approach is feasible for handling protein structures. Exploiting computational approaches, I am exploring a key feature in protein structures, developing a program to extract the feature, classifying proteins according to the extracted features and compiling the proteins into a database.


(1) Protein functions and structural changes

A protein folds into a structure and performs a function. However, since proteins are not static molecules, their structures change constantly. To grasp structural changes of various proteins and explore the relationships between the structural changes and protein functions, I have been developing a program to describe protein structural changes, classifying the structural changes and analyzing their functional annotations using Protein Data Bank (PDB), UniProt and other databases.

(2) Analysis and development of methods to compare protein sequences or structures

In the field of protein science, a comparison tool of protein sequences or structures is one of the most fundamental ones. The task of comparing protein sequences and structures and estimating their similarities can be considered to be an optimization problem and be reformulated in a framework of statistical mechanics. I proposed a novel formulation of a sequence or structure comparison method and developed a more sensitive tool to detect sequence or structural similarities.

Future work

In living bodies, more complex functions are achieved not by a single protein molecule but by a number of proteins. I aim at a comprehensive understanding of such complex biological functions organized by a number of protein molecules, i.e., a molecular system, using various computational tools and databases.




  • 2003, Dr. of Science, Kyoto University.
  • 2003, Researcher, Osaka University.
  • 2005, Researcher, Yokohama City University.
  • 2005, Researcher, Tokyo Institute of Technology.
  • 2008, Researcher, Nagoya University.
  • 2009, Designated Assistant Professor, Nagoya University.

Academic Societies

  • The Biophysical Society of Japan
  • Protein Science Society of Japan


  1. R. Koike, et al. Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. J. Mol. Biol. 379, 397-401 (2008)
  2. R. Koike, et al. Alteration of oligomeric state and domain architecture is essential for functional transformation between transferase and hydrolase with the same scaffold. Protein Sci. 10, 2060-2066 (2009)
  3. R. Koike, et al. Probabilistic description of protein alignments for sequences and structures. Proteins. 56, 157-166 (2004)