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Open Access Database

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides

Anita Sarkar12 and Serge Pérez123*

Author affiliations

1 Centre de Recherches sur les Macromolécules Végétales (CERMAV*) Centre National de la Recherche Scientifique, Grenoble Cedex 9, BP 53X, F-38041, France

2 Université Joseph Fourier, Grenoble, France

3 European Synchrotron Radiation Facility, (ESRF), Grenoble, France

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Citation and License

BMC Bioinformatics 2012, 13:302  doi:10.1186/1471-2105-13-302

Published: 14 November 2012

Abstract

Background

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol.

Description

PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available.

Conclusion

PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr webcite.

Keywords:
Polysaccharides; Carbohydrates; Three-dimensional (3D) database; Graphical user interface (GUI); Atomic coordinates; Information portal