Notes from the Design Study 4 (NMR) meeting
Utrecht December 1st, 2005
Present:
Roland Stenutz, roland@organ.su.se, Coordinator of DS-4, Stockholm University
Martin Frank, m.frank@chem.uu.nl, Bas Leeflang, b.r.leeflang@chem.uu.nl, Hans Kamerling, j.p.kamerling@chem.uu.nl, Hosts, participants DS4, Bijvoet Center, University of Utrecht
Matthias Studer, matthias.studer@unibas.ch,Participant DS4, University of Basel
Wim Vranken, wim@ebi.ac.uk, Invited guest, CCPN, EBI
1015-1230 Presentations
Martin Frank started the meeting by welcoming everybody.
Roland Stenutz presented CASPER and some of the recent work that had been done to connect CASPER to the chemical shift prediction tool being developed at Heidelberg. Bas Leeflang gave an overview of the objectives of EUROCarbDB and DS4 in particular. The principles of the Glycosicences.de NMR prediction were presented by Martin Frank followed by a talk about progress in the development of NeuroCarb by Matthias Studer. NeuroCarb now supports galactose, glucose and mannose with fucose and xylose in the pipeline.
1230-1330 Lunch and tour of the NMR facilities
1330-1400 Presentation of CCPN
Wim Vranken presented the CCPN-project. CCPN is a data model and API for the processing of NMR data. It shares parts with other ‘Collaborative Computing Projects’, e.g. CCP4 (protein crystallography). Wim had prepared a few simple glycosyl residues to demonstrate some NMR-tools built on the CCPN API. The possibility of creating a more complete system for glucans was discussed. One of the requirements was a clear definition of carbohydrate residues that could be implemented in the CCP-data model. (This would affect crystallography as well?)
The remainder of the afternoon was spent discussing various aspects of encoding glycosyl residues and how EUROCarbDB may benefit from the CCPN. It was felt that both the CCPN and EUROCarbDB would benefit from collaboration and that the amount of additional work would be very modest.
The following was agreed at the meeting:
DS4 will continue discussions with CCPN on the possible extension of the CCPN data model to carbohydrates. Before proceeding an agreement on the description of glycosyl residues has to be reached within EUROCarbDB.
DS4 will develop XML-representations of processed NMR-data with and without assignments. Apart from the NMR data itself, encoding the assignments requires the residues to be labelled so that they can be referred to. Encoding the NMR-peaks as part of ‘residues’ was found to be inadequate for peaks that arise from nuclei in separate residues. An advantage of keeping the NMR data separate from the structure is that either may be modified independently.
Before any further progress in DS4 can be made it is necessary that an agreement on the description of carbohydrate structures is reached with the consortium.
EuroCarbDB is a Research Infrastructure Design Study
Funded by the 6th Research Framework Program of the European Union
(Contract: RIDS Contract number 011952)
