rapidly converts the primary sequence of a complex carbohydrate, as defined by standard nomenclature, directly into a reliable 3D molecular model by linking together preconstructed 3D molecular templates of monosaccharides in the manner specified by the sequence and then optimizing the 3D structure using the MM3 force field.
is a data base system for the management of conformational maps and profiles, The system allows conformational maps to be archived in a standard format, and it will provide search and comparison facilities. An interface to structures from Sweet-DB is implemented. We also offer scientists the possibility of adding their own publicized structures to the database via a web interface.
Dynamic Molecules is the first Internet portal which provides interactive access to the techniques of molecular dynamics simulations and tutorials via standard Web technologies and using only publicly available software. The 'expert mode' has been specially developed to explore the conformational space of oligosaccharides.
Visualization of chemical 3D structures on the web comes with problems because the web browser cannot display chemical structures without the help of additional software. If you create a page with a 3D structure of a molecule and the visitor of your page does not use this special viewer software for displaying molecules it cannot get the whole information of the page which should be meditated.
PDB2MultiGIF takes the 3D structure and generates an animated image which can be displayed using any browser. Thus every visitor of your page can get the whole information.
performs an in silico glycosylation of proteins. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II.
Commonly, computational methods, which explore the conformational space of oligosaccharides, are discussed in conjunction with experimental results mostly derived from NMR data. The nuclear Overhauser enhancement (NOE) allows one to detect the proximity in space between protons that may be located in different, yet spatially neighbouring residues of oligosaccharides.
The DISTANCE MAPPING approach allows to draw distances of equal r as a function of the appropriate F,Y coordinates. A single pair of contours drawn for the lower and upper limits of r for one NOE encloses a torus-like region which still covers an infinite number of F,Y conformations.