CARBOHYDRATES

red_bullet.gif (914 bytes) Sweet (German Cancer Research Center Heidelberg) - is a program for constructing 3D models of saccharides from their sequences.

red_bullet.gif (914 bytes) GLYCAM Builders (Robert J. Woods, Complex Carbohydrate Research Center, University of Georgia, U.S.A.) - this group uses computational techniques of molecular dynamics (MD) and free energy perturbation simulations to elucidate the conformational properties of oligosaccharides. The computational simulations use the all-atom AMBER force field for proteins and nucleic acids and a novel set of parameters developed by Dr. Woods's group for use with carbohydrates, GLYCAM. The GLYCAM parameters make it possible to probe the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics and compare these directly with experimental NMR data that are often consistent with numerous possible conformations.
 

red_bullet.gif (914 bytes) Glycosciences.de - provides bioinformatics tools for glycobiology and glycomics:

 Glycofragment - calculates and displays the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MSspectra.   

 LiGraph - generates schematic drawings of oligosaccharides which are often used to display glycan structure. 

 pdb2linucs - automatically extracts carbohydrate information from pdb-files and displays it using the LINUCS-Code.    

 LINUCS - LInear Notation for Unique description of Carbohydrate Structures  
 
 GlySeq - provides statistical analyse the sequences around glycosylation sites.    

 GlyTorsion - performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank.  
 
 GlyVicinity - generates statistics about the amino acids present in the vicinity of carbohydrate residues.  

 carp - generates Ramachandran-like plots of carbohydrate linkage torsions in pdb-files.  
 
 pdb-care - checks carbohydrate residues in pdb-files for errors.