Laboratory of Protein Informatics


Associate Professor
Akira R. KINJO
mail akinjo at
Visiting Associate Professor
Yasushige YONEZAWA
mail yasuyon33 at
Visiting Associate Professor
mail syama at
Assistant Professor
mail ytakano at

Structual Infomation Biology


Institute for Protein Research, The Research Center for Structural and Functional Proteomics


3-2 yamadaoka, Suita, Osaka 565-0871, JAPAN

Research Theme

Our laboratory, Laboratory of Protein Informatics, is engaged in the protein informatics researches by developing the international protein structural databases and the structural bioinformatics covering molecular modeling and design. We also perform large scale simulation calculations by parallel computers to examine free energy landscapes and biochemical functions of biomolecular systems with molecular dynamics and quantum chemistry simulations.

Protein Structural Bioinformatics

1. Protein Structural Databases and Analysis

1-1) Construction and maintenance of international protein structural database, PDB, collaborating with RCSB-PDB in USA and PDBe-EBI in EU, as the Protein Data Bank japan (PDBj). 1-2) Structural bioinformatics covering molecular modeling and design, making new databases and Web services: Protein Globe, for a global view and representation of the protein fold universe; eF-seek, for rapid search of protein surface similarity with the physicochemical properties using the geometric hashing method; GIRAF, for similarity search of ligand binding structural motifs; Piranha, for prediction of RNA-binding residues from protein sequence information; and SASab, for Structural and sequence Analysis System for AntiBody research. In addition, as the structural bioinformatics study, many protein-protein interactions are analyzed and predicted, participating the CAPRI contest

Protein Structural Bioinformatics

2. Protein Molecular Simulations

Development of our own molecular simulation system for large-scale parallel computers to examine electronic and atomic structures of biomolecular systems for the reaction energies and free energy landscapes with the hybrid QM (Quantum mechanics) / MD (Molecular dynamics) method.

0The top page of PDBj (Protein Data Bank Japan: For maintaining the database of the protein structures, PDBj manages the international database, wwPDB, collaborating with the Research Collaboratory for Structural Bioinformatics (RCSB-PDB) and the European Bioinformatics Institute (PDBe-EBI) in EU. In addition, PDBj continues its own research and development of protein structure databases.

1Similar atomic structures and network of the structural motifs of the ligand binding sites. An example of the connected component of the similarity network and several folds examples of structural motifs shared by different protein folds. The superimposed similar ligand binding sites are shown in CPK colors and pink, and the associated ligands are shown in CPK and green. (Kinjo, A. R. Structure 17, 234-246, 2009)

2The free energy landscape of the Ace-Pro-NMe in explicit water as a function of the pyramidality and the reaction coordinate ω’ (O-C-N-Cδ) for the cis-trans isomerization of the peptide bond, analyzed by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. Our study shows that the prolyl isomerization in water can utilize the intra- and intermolecular hydrogen bonds as a proton donor, gaining stability for the pyramidalized transition state. (Yonezawa, Y., J. Ame. Chem. Soc. 131, 4535-4540, 2009)


Kinjo, A. R., Nakamura, H., Comprehensive Structural Classification of Ligand- Binding Motifs in Proteins Structure 17 , 234 - 246 (2009)

Yonezawa, Y., Nakata, K., Sakakura, K., Takada, T., Nakamura, H Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline di-peptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water Journal of the American Chemical Society 131 , 4535 - 4540 (2009)

Takano, Y., Nakamura, H. Quantum mechanical study of the proton transfer via a peptide bond in the novel proton translocation pathway of cytochrome c oxidase. Chemical Physics Letters 430 , 149 - 155 (2006)

Berman, H., Henrick, K., Nakamura, H., Markley, J. L. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research 35 , D301 - D303 (2007)


Haruki Nakamura, Dr.
Professor, Laboratory of Protein Informatics
Institute for Protein Research,
The Research Center for Structural and Functional Proteomics,
Osaka University,
3-2 Yamadaoka, Suita,
Osaka 565-0871,