A Database of Polysachharide 3D structures

By A. Sarkar & S. Pérez


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The POLYS computer program has been developed to generate three-dimensional structures of polysaccharides and complex carbohydrates from their primary sequence reference-in-status-bar. POLYS combines a database of monosaccharide structures with a database containing population information on disaccharide fragments using an approximation of independent neighboring glycosidic linkages. A primary structure in simple ASCII syntax is transformed by the program into Cartesian coordinates, which can be exported to frequently used formats. Also, the program can generate Boltzman distributions of polysaccharide conformations from which configurational macroscopic properties such as persistence length and radius of gyration can be calculated and compared to experimental values derived from viscometry, light- and neutron scattering studies. The program has been successfully applied to the study of configurational and conformational properties of heparin, and in structurally exploring pectic polysaccharides (both the homo- and the rhamnogalacturonan backbone, and the organization of arabinan and arabinogalactan side chains on the latter).


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