POLYSAC is an annotated data base that contains,
at the present time, the 3D structural information of about 150 entries.
This data base is a subset of a larger data base entitled “Polysac3DB”
(http://polysac3db.cermav.cnrs.fr) which entries have been established experimentally from X-ray,
neutron electron diffraction, high resolution NMR and molecular modelling.
These data have been collected from an extensive screening of scientific literature,
covering 50 years of experimental research (A. Sarkar & S. Perez, BMC Bioinformatics 2012,
13:302).
The polysaccharides have been systematically organized using standard names in the field of
carbohydrate research into 18 categories representing polysaccharide families.
Agarose
Alginates
Amylose and Starches
Bacterial Polysaccharides
Carrageenans
Celluloses
Chitins and Chitosans
Curdalsn
Glycosaminoglycans (GAG)
Galactoglucans
Galactommans
Glucomannans
Mannans
Pectins
Scleroglucans
Xylans
Nigeran
Others (including inulin)
Provision is made to create sub-families, an option that is likely to be useful in the case of bacterial polysaccharides.
Data Query
The database is available from Glyco3D.
Upon reaching the search page, two buttons to query the data base appear on the left
hand panel: Simple search and Advanced search.
Simple Search
A search box is provided, in which the user selects from the name of the polysaccharide of
interest, available through a drop-down button that enlists all the polysaccharides
present in the data base. The selection involves first a choice of the family and
second the choice of the sub-family.
The result indicates the sequence of the repeating unit of the polysaccharide, following the nomenclature established for the Glyco3D portal.
Advanced Search
Upon selecting “Select Criteria”, two search boxes appear offering the choice between
the sequence of the repeating unit and the method of investigation used in the
determination of the 3D structure. Selecting the “sequence option” opens a drop-down
button that enlists all the sequences present in the data base.
The user may want to combine the two selection criteria.
Results
In the first level of results the sequence of the repeating unit,
along with the family, subfamily and origin are given and offer the choice to
fetch more information. The detailed results are organized under two tabs:
“Molecule Information” and “View and Download”.
Molecule Information
This includes the trivial name of the polysaccharide, its sequence,
the graphical representation of the stereo-chemical configuration,
the symbolic notation for carbohydrates, the experimental method to solve the structure,
the origin and the bibliographical reference. A link to the Polysac3DB data base is offered
to gather further information.
Display and Download
The molecules are displayed under Jmol applet windows that enable basic viewing and
measurements options, under the right-click options. Depending upon the cases, up
to three types of 3D structures are given, corresponding respectively to the repeating
unit, the polysaccharide chain, and the crystalline packing.
Each of the structures can be downloaded from this section,
the coordinate files being at the PDB format.