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. 2002 Jan 1;30(1):405-8.
doi: 10.1093/nar/30.1.405.

SWEET-DB: An Attempt to Create Annotated Data Collections for Carbohydrates

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Free PMC article

SWEET-DB: An Attempt to Create Annotated Data Collections for Carbohydrates

Alexander Loss et al. Nucleic Acids Res. .
Free PMC article

Abstract

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/.

Figures

Figure 1
Figure 1
Structure-oriented retrieval of (sub)structure. Input of the topology information is accomplished using 1 × 4 input matrix (top right). Monosaccharides and linkage information can be input using pull-down menus. Eleven structures were found containing the α-d-Galp-(1–2)-α-d-Galp substructure. Topology of first three hits is displayed on the left. Activating the ‘3D Co-ordinates’ button invokes the transfer of a file containing co-ordinates which can be visualized using an appropriate plugin or helper application. Here RASMOL as external helper application is used to display a stereo model of the trisaccharide. Thus, the user has the possibility to look at the structure in different orientations. Activating the ‘Explore’ button will display all data stored for that sequence.
Figure 2
Figure 2
Using the spreadsheet (top left), all entries having a specific atom (e.g. H-1) in a specific residue (e.g. α-d-Galp) can be retrieved and displayed as frequency-shift histogram (bottom left). Additionally, the shift range of interest can be specified. A list of all entries fulfilling the query is provided. Here only one example is displayed (top right). The complete NMR spectra for this sequence can be recalled. The NMR data are provided as a list of assigned shifts and coupling constants (bottom right).

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