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Protein Data Bank Development Lab
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The lab works with partners around the world to operate databases of protein three-dimensional structures and related data.
AboutAbout the lab
Working with partners around the world to operate a data bank of three-dimensional structures
The Protein Data Bank Development Lab is part of the Center for Advanced Protein Data Science, affiliated with the Institute for Protein Research at Osaka University, and handles work related to maintaining life science databases such as PDBj.
PDBj (Protein Data Bank Japan) is one of the organizations that operate the PDB, which collects three-dimensional structural information on molecules such as proteins, and the EMDB, which collects information on Coulomb potential maps obtained by electron microscopy.
Under the wwPDB (worldwide Protein Data Bank), PDBj works with RCSB PDB and BMRB in the US and PDBe and EMDB in Europe to operate a single, unified PDB/EMDB for the world.
In addition, the lab is active in the BMRBj, EMPIAR Japan site, BSMA, and XRDa groups.
Key terms
- PDB
- A database collecting information on the three-dimensional molecular structures of biological macromolecules such as proteins (Protein Data Bank).
- wwPDB
- The worldwide Protein Data Bank. Organizations such as PDBj cooperate under it to operate a single PDB/EMDB for the world.
- NMR
- Nuclear magnetic resonance. One of the methods used to study information on biological macromolecules.
ResearchResearch themes
The lab handles work related to maintaining life science databases in cooperation with organizations in Japan and abroad. It has groups for PDBj, BMRBj, the EMPIAR Japan site, BSMA, and XRDa.
*Illustrative imageProtein Data Bank Japan (PDBj)
PDBj is one of the organizations that operate the PDB, which collects three-dimensional structural information on molecules such as proteins, and the EMDB, which collects information on Coulomb potential maps obtained by electron microscopy. In Japan, it also works with DBCLS and DDBJ on activities related to the use of life science databases.
*Illustrative imageBMRBj, the NMR Data Bank
BMRB is a database of information on biological macromolecules studied by NMR (nuclear magnetic resonance). The lab works with the original site at the University of Connecticut on deposition processing and tool development, and operates a mirror site in Japan.
*Illustrative imageArchive of Raw Electron Microscopy Images
EMPIAR is a database of the raw images used to solve molecular structures by electron microscopy, and is operated by the European Bioinformatics Institute. Since 2018, the lab has operated its Japanese mirror site.
*Illustrative imageBiological Structure Model Archive (BSMA)
The lab handles BSMA, an archive that collects models and simulation data of biomolecules obtained through calculations such as molecular dynamics, docking, and homology modeling.
MembersFaculty
The members of the Protein Data Bank Development Lab consist of faculty members, visiting faculty members, project researchers, technical specialists, and project administrative staff.As of 2026
- ProfessorGenji Kurisu
- Project Associate ProfessorTakanori Nakane
- Project Associate ProfessorJian Yu
- Project LecturerBEKKER Gert-Jan
- Project Assistant ProfessorKoya Sakuma
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Report an errorAbout the images
The top and research theme images are illustrative and were not taken at the lab. They are cropped from Wikimedia Commons images. Cropped CC BY-SA images are provided under the same CC BY-SA license as the original (version shown on each line).
- Top image: “Neuraminidase Ribbon Diagram” NASA / Public domain (cropped)
- Protein Data Bank Japan (PDBj): “Structure of TAZ-TEAD complex (Mouse) - Protein Data Bank” Protein Data Bank (PDB) / CC0 (cropped)
- BMRBj, the NMR Data Bank: “2k5d NMR ensemble ribbons” Jane Richardson (Dcrjsr) / CC BY 3.0 (cropped)
- Archive of Raw Electron Microscopy Images: “Cryo-EM image of C. thermophilum lysate” Pkastrit / CC BY-SA 4.0 (cropped)
- Biological Structure Model Archive (BSMA): “Sampling in Monte Carlo and molecular dynamics” Qx8314 / CC BY 4.0 (cropped)
- Related lab (計算生物学研究室
（水口研） ): “Linuron-3D-molecular-model-engraved-render-CAS-330-55-2” MolGod Scientific / CC BY-SA 4.0 (cropped) - Related lab (生体分
子動態モデリング研究室 （TIWARI研） ): “TriosePhosphateIsomerase Ribbon pastel” Dcrjsr / CC BY 3.0 (cropped) - Related lab (細胞機能
デザイン研究室 （戸田研） ): “Synthetic Biology Research at NASA Ames” Alexander van Dijk from San Francisco, United States / CC BY 2.0 (cropped) - Related lab (細胞システム研究室
（岡田研） ): “Fluorescence micrograph of Thalassiosira nanae” Terry J. McGenity, Amare Gessesse, John E. Hallsworth, Esther Garcia Cela, Carol Verheecke-Vaessen, Fengping Wang, Max Chavarría, Max M. Haggblom, Søren Molin, Antoine Danchin, Eddy J. Smid, Cédric Lood, Charles S. Cockell, Corinne Whitby, Shuang-Jiang Liu, Nancy P. Keller, Lisa Y. Stein, Seth R. Bordenstein, Rup Lal, Olga C. Nunes, Lone Gram, Brajesh K. Singh, Nicole S. Webster, Cindy Morris, Sharon Sivinski, Saskia Bindschedler, Pilar Junier, André Antunes, Bonnie K. Baxter, Paola Scavone and Kenneth Timmis Photograph by Philippe Laissue. / CC BY-SA 4.0 (cropped)
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