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.
Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including (1)H, (13)C and (15)N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001-2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.
Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871 Osaka, Japan. naohiro@protein.osaka-u.ac.jp
Naohiro
N
Kobayashi
Yoko
Y
Harano
Naoya
N
Tochio
Eiichi
E
Nakatani
Takanori
T
Kigawa
Shigeyuki
S
Yokoyama
Steve
S
Mading
Eldon L
EL
Ulrich
John L
JL
Markley
Hideo
H
Akutsu
Toshimichi
T
Fujiwara
D030562:Databases, Protein; D023281:Genomics / Q000379:methods; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods; D011786:Quality Control; D012984:Software
D011506:Proteins