GlyNest and CASPER: two independent approaches to estimate 1H and 13C NMR shifts of glycans available through a common web-interface.

GlyNest and CASPER (www.casper.organ.su.se/casper/) are two independent services aiming to predict (1)H- and (13)C-NMR chemical shifts of glycans. GlyNest estimates chemical shifts of glycans based on a spherical environment encoding scheme for each atom. CASPER is an increment rule-based approach which uses chemical shifts of the free reducing monosaccharides which are altered according to attached residues of an oligo- or polysaccharide sequence. Both services, which are located on separate, distributed, servers are now available through a common interface of the GLYCOSCIENCES.de portal (www.glycosciences.de). The predictive ability of both techniques was evaluated for a test set of 155 (13)C and 181 (1)H spectra of assigned glycan structures. The standard deviations between experimental and estimated shifts ((1)H; 0.081/0.102; (13)C 0.763/0.794; GlyNest/CASPER) are comparable for both methods and significantly better than procedures where stereochemistry is not encoded. The predictive ability of both approaches is in most cases sufficiently precise to be used for an automatic assignment of NMR-spectra. Since both procedures work efficiently and require computation times in the millisecond range on standard computers, they are well suited for the assignment of NMR spectra in high-throughput glycomics projects. The service is available at www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation.

SWEET-DB: an attempt to create annotated data collections for carbohydrates.

Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use modern web techniques to annotate and/or cross-reference carbohydrate-related data collections which allow glycoscientists to find important data for compounds of interest in a compact and well-structured representation. Currently, reference data taken from three data sources can be retrieved for a given carbohydrate (sub)structure. The sources are CarbBank structures and literature references (linked to NCBI PubMed service), NMR data taken from SugaBase and 3D co-ordinates generated with SWEET-II. The main purpose of SWEET-DB is to enable an easy access to all data stored for one carbohydrate structure entering a complete sequence or parts thereof. Access to SWEET-DB contents is provided with the help of separate input spreadsheets for (sub)structures, bibliographic data, general structural data like molecular weight, NMR spectra and biological data. A detailed online tutorial is available at http://www.dkfz.de/spec2/sweetdb/nar/.