Laboratory of Protein Databases

At Institute for Protein Research, Osaka University, we maintain databases involved in life science such as PDBj (Protein Data Bank Japan). The target databases are described below:


PDBj (Protein Data Bank Japan) is a partner to manage PDB, which includes molecular structural information of biological macromolecular such as proteins. Under wwPDB (World Wide Protein Data Bank), we collaborate with RCSB PDB in the USA, PDBe in EU, BMRB in the USA to manage the worldwide unique PDB.

In Japan, we facilitate on utilizing life science databases collaborating with DBCLS (Data Base Center for Life Science) and DDBJ (DNA Data Bank Japan) under the support of 1. To promote this activity, we founded a common work framework JBI (Japan alliance for Bioscience Information).


BMRB (Biological Magnetic Resonance data Bank) is a database including various information about biomolecules studied by NMR (Nuclear Magnetic Resonance). Under the support of 1, we collaborate with the group in the University of Wisconsin-Madison to accept deposition, develop various tools and maintain the Japan site of BMRB.

CCDCCSD: The CCDC's National Affiliated Centre (NAC) in Japan

CSD (Cambridge Structural Database) is the database of crystal structures about organic and organic metal compounds provided from CCDC (Cambridge Crystallographic Data Centre). In Japan, the CCDC's National Affiliated Centre (NAC) is placed in Institute for Protein Research, Osaka University and we provide services for academic CSD users. While for enterprise users, JAICI (Japan Association for International Chemical Information) is the contacts point.


EMPIAR (Electron Microscopy Public Image ARchive), managed by EBI (European Bioinformatics Institute), is the raw image database to construct molecular structural information studied by electron microscopy. In 2018, we started to provide a mirror site of EMPIAR at Japan under the support of 2.

Biological Structure Model Archive (BSM-Arc, BSMA)Biological Structure Model Archive (BSM-Arc, BSMA)

Biological Structure Model Archive (BSM-Arc, BSMA) is an archive to collect data obtained via in-silico methods related to structural biophysics (such as structure models or simulations).

  1. "JST-NBDC" (National Bioscience Database Center, Japan Science and Technology Agency) and "the MEXT grants for joint usage and research center assigned to Institute for Protein Research (IPR), Osaka University"
  2. BINDS (Basis for Supporting Innovative Drug Discovery and Life Science Research)