W3-SWEET: Carbohydrate Modeling By Internet

Abstract

  The software tool SWEET accessible through Internet is described which rapidly converts the commonly used sequence information of complex carbohydrates directly into a preliminary but reliable 3D model. The basic idea is to link preconstructed 3D molecular templates of monosaccharides in a specific way of binding as defined in the sequence information. In a subsequent step a fast routine to explore the conformational space for each glycosidic linkage has been implemented. Systematic rotations around the glycosidic linkages are performed, calculating the van der Waals interactions for each step of rotation. The user interaction is supported by an input spreadsheet consisting of a grid of sugar symbol and connection type cells. Several ways to visualise and to output the generated structures and related information are implemented. Since interactivity is an absolute prerequisite for each WWW application, the limitations of the approach are discussed in detail. SWEET will open modelling techniques to a broader range of users, especially for those who do not have access to the required hard- and software equipment.