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Database Partners

Protein Data Bank in Europe

Aleksandras Gutmanas, Pieter Hendrickx and Gerard J. Kleywegt, European Bioinformatics Institute, Hinxton, UK
The PDBe group have been a core part of the CCPN project since its inception, helping to define data standards and generating key components of the CCPN software including; FormatConverter, DataShifter, the Entry Completion Interface and chemical compound (ChemComp) resources. For more information please visit the PDBe NMR pages.

Biological Magnetic Resonance Bank

John Markley & Eldon Ulrich, University of Wisconsin, Madison, WI, USA

CCPN has a long-standing collaboration with the BMRB to allow seamless exchange between CCPN projects and the NMR-STAR data format used for archival in the BMRB database. Much of this work has been done by developers at the PDBe; Wim Vranken and Chris Penkett. This collaboration ensures that the NMR-STAR schema and the CCPN data model are synchronised to allow near lossless conversion between the two systems. A good example of this is the NMR Restraints Grid where the restraints are available as CCPN projects.
To help with the deposition of NMR data at the BMRB via the ADIT-NMR system, the Entry Completion Interface (Penkett/PDBe) had been developed and is available from within CcpNmr Analysis. See the Deposition section of the Extend-NMR project for more details.


Selecting data for BioMagResBank deposition via CcpNmr ECI


A project designing databases and bioinformatics tools for glycobiology and glycomics
The EUROCarbDB project combined glycomics data into a single database resource, collating from various experimental sources, including mass spectroscopy, HPLC and NMR. The NMR related data is stored as CCPN projects within the EUROCarbDB infrastructure, and thus conforms to the CCPN data model. The NMR data is accessible via the CCPN Java API, as well as through database queries. Note the EUROCarbDB project is not currently funded.
One of the EUROCarbDB partners is the Widmalm group at Stockholm University, who have produce the CASPER software. CASPER is seamlessly linked to CCPN, given that it can directly read and write CCPN projects; the results are immediately visible in CcpNmr Analysis. CASPER is used to determine the chemical structure and/or sequence of saccharides using chemical shift data. 13C and 1H spectra are simulated for a given chemical structure to allow identification and assignment. Also poly- or oligo-saccharide sequences can be determined using sugar and methylation data, as well as the NMR shifts.

The EUROCarbDB interface to CASPER