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A complex carbohydrate structural database

Objective

The CarbBank project has been an international effort to supply scientists working in the carbohydrate field with information on complex oligosaccharide structures, mostly of biologically relevant compounds. Besides the three European partners, scientific groups in the USA and Japan were included in the collaboration. The group in the USA, the Complex Carbohydrate Research Center (CCRC) has also been responsible for the development of the database management program and assembly of the associated database CCSD.
The CarbBank project has been concerned with the establishment of the Complex Carbohydrate Structural Database (CCSD), containing published oligosaccharide structures higher than disaccharides with biological importance and the accompanying database management program CarbBank. Additionally, investigation in connecting spectroscopic information like 1H-NMR and 13C-NMR data to the structural database has been achieved by the establishment of the NMR database SUGABASE.
Release number 14 of the CCSD contains 37,127 records of which 11,000 are unique oligosaccharide structures as underivatized trisaccharides and higher. Most of the published literature on carbohydrates up to 1995 has been included and the database is almost up to date. The database and the management program are available either on the Data Repository CD-ROM among other databases distributed by the National Center of Biotechnology Information (NCBI), Washington, DC or on CD-ROM together with the protein sequence database ATLAS from the Max-Planck Institute of Biochemistry (MIPS) in Martinsried. Furthermore, the database is accessible over the Internet by anonymous FTP from a public NCBI server.
By the end of January 1996 the database SUGABASE contained 1,595 carbohydrate structures described by 1,250 1H-NMR and 539 13C-NMR records. The program can be obtained as a Unix-Version running on Silicon Graphics and as well as a PC-version running under Windows or Linux. The database and the program are distributed on floppy disks or are available over the Internet at URL ftp://bocftp.chem.ruu.nl/pub/sugabase.

MAJOR SCIENTIFIC BREAKTHROUGHS:
The efforts in building the CCSD have been very successful through the collaboration between the american and european partners, with about 37,000 records, the size of the database is larger than anticipated and almost up to date. The database has been well accepted and has been distributed worldwide. Due to enormous amount of structures searchable by CarbBank the database has recently been chosen at a 'Workshop to establish databases of carbohydrate spectra' in Seattle during the XIIIth International Symposium on Glycoconjugates to serve as reference for the development of further databases. These databases are planned to contain Mass-spectral data as well as NMR-data accessible via Internet.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

CARLSBERG LABORATORY
Address
10,Gamle Carlsberg Vej 10
2500 Valby
Denmark

Participants (2)

UNIVERSITY OF HAMBURG
Germany
Address
Martin-luther-king-platz 6
20146 Hamburg
UTRECHT UNIVERSITY
Netherlands
Address
8,Padualaan 8
3584 CH Utrecht