Deposition of NMR structures of small biomolecules and their data to database PDBj-BMRB


Eiichi Nakatani1,2, Takanori Matsuura2, Steven Mading3, Yoko Harano2, Naohiro Kobayashi2, Eldon. L. Ulrich3, John L. Markley3, Hideo Akutsu2, Haruki Nakamura2, Toshimichi Fujiwara2

1BIRD, Japan Science and Technology Agency
2Instutute for Protein Research, Osaka University
3BMRB, University of Wisconsin Madison

The 3rd Asia-Pacific NMR Symposium (Jeju, Korea, 2009.10.25 - 2009.10.28)

BMRB (Biological Magnetic Resonance Data Bank) is the database for experimental parameters derived from NMR spectroscopic investigations on the biological macromolecules such as assigned chemical shifts. The total number of BMRB entries reached up to 5766 in September, 2009.

PDBj-BMRB (BMRB group in Protein Data Bank Japan) operates the BMRB website (http://bmrb.prtein.osaka-u.ac.jp) in collaboration with BMRB in USA. In 2008, about 25% of total entries were processed by PDBj-BMRB in Osaka University. PDBj-BMRB has web-pages in local languages (http://bmrbdep.protein.osaka-u.ac.jp/index_en.html) to facilitate data collection especially from Asia and Oceania regions.

Data input web page of SMSDep

Figure 1 Data input web page of SMSDep

In this autumn, PDBj-BMRB will feature website SMSDep (Small Molecule Structure Deposition) for accepting not only chemical shifts but also NMR structures of small molecules such as peptides less than 24 residues. PDB (Protein Data Bank) accept no more such small biomolecular structures. Thesemolecules, however, have important biological functions such as signal transduction based on the structures. Therefore, the data collection of these NMR structures would contribute to structural biology and its application to drug design. In this database, a PDBj annotator group validates all the NMR structures from the world. Thus PDBj including its BMRB group in Osaka plays a crucial role in this database for NMR structures of small biomolecules. We are developing the SMSDep website by building a new network of data server systems in Osaka and Madison, which facilitates the convenient and secure database activity.



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MATSUURA Takanori
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