Laboratory of Protein Databases

Member

Director Haruki NAKAMURA
Genji KURISU
Toshimichi FUJIWARA
Associate Professor Akira KINJO
Naohiro KOBAYASHI
Assistant Professor Hirofumi SUZUKI
Technical Staff Takashi KOSADA

Correspondence

Tel 81-6-6879-4311
Fax 81-6-6879-8636
E-mail
URL

Research

PDBj Group

【Member】
Professor  Genji KURISU, Haruki NAKAMURA
Associate Professor  Akira R. KINJO
Assistant Professor  Hirofumi SUZUKI
Tecnical Staff  Takashi KOSADA

【Correspondence】
Tel: 06-6879-4311
Fax: 06-6879-8636
E-mail:
URL: https://pdbj.org/

【Research】
We, PDBj, curate, edit and process the 3D atomic structure data of biological macromolecules such as proteins and nucleic acids, and provide them freely and publicly from our own Web site, collaborating with wwPDB (worldwide PDB: https://wwpdb.org/) as one of the members of wwPDB. We also prepare various services for researchers and students, who are interested in structural biology. (Refs. 1, 2): Molecular graphics viewer, jV, molecular surface database for functional sites, eF-site, with the eF-seek service for the search of similar molecular surface, GIRAF, query service for the similar ligand binding sites, the navigation of the sequence and structure neighbours, Spanner, homology modeling server, and EM Navi, image viewer for the structures by electron microscopy.

 

PDBj-BMRB Group

【Member】
Professor  Toshimichi FUJIWARA
Visiting Professor Chojiro KOJIMA
Associate Professor Naohiro KOBAYASHI

【Correspondence】
Tel: 06-6879-8598
Fax: 06-6879-8599
E-mail:
URL: http://bmrbdep.protein.osaka-u.ac.jp/index_en.html

【Research】
We, PDBj-BMRB, collect and process the NMR experimental data of biological molecules, and provide them from our Web site, collaborating with BMRB at University of Wisconsin-Madison in USA. (Ref. 1).
BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scientists in their analysis of the structure, dynamics, and chemistry of biological systems and to support further development of the field of biomolecular NMR spectroscopy.

 

CSD(Cambridge Structural Database) Group

【Member】
Professor  Haruki NAKAMURA

【Correspondence】
Tel: 06-6879-4311
Fax: 06-6879-8636
E-mail:
URL: http://www.protein.osaka-u.ac.jp/csd/csd.html

【Research】
We support Academia researchers in Japan, who want to use CSD (Cambridge Structural Database system), which is a database for small organic chemical compounds constructed by CCDC (Cambridge Crystallographic Data Centre). We also provide a portal for CSD to researchers inside and even outside of Osaka University.

Current Research Programs

References

PDBj (Protein Data Bank Japan) Group

  1. Protein Data Bank Japan (PDBj): Maintaining a structural data archive and Resource Description Framework format. Kinjo AR, Suzuki H, Yamashita R, Ikegawa Y, Kudo T, Igarashi R, Kengaku Y, Cho H, Standley DM, Nakagawa A, Nakamura H. Nucleic Acids Research 40:D453-D460 (2012)
  2. PDBj Mine: Design and implementation of relational database interface for Protein Data Bank Japan. Kinjo AR, Yamashita R, Nakamura H. Database 2010:baq021 (2010)

PDBj-BMRB (BioMagResBank) Group

  1. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. Markley JL, Urich EL, Berman HM, Henrick K, Nakamura H, Akutsu H. Journal of Biomolecular NMR 40:153-155 (2008)
  2. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database. Kobayashi N, Harano Y, Tochio N, Nakatani E, Kigawa T, Yokoyama S, Mading S, Ulrich EL, Markley JL, Akutsu H, Fujiwara T. Journal of Biomolecular NMR, in press.