3D Structure related tools

3D Structure modeling

Sweet-II
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.

GlyProt
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.

Detection and Validation of Carbohydrates in PDB files

PDB CArbohydrate REsidue check (pdb-care)
checks carbohydrate residues in PDB files for errors

pdb2linucs
detects carbohydrate residues in PDB files

Carbohydrate Ramachandran Plot (CARP)
generates Ramachandran-like plots of carbohydrate linkage torsions in pdb-files.

Statistical analysis of carbohydrate properties derived from the Protein Data Bank (PDB)

GlyTorsion
performs a statistical analysis of carbohydrate torsion angles derived from the Protein Data Bank. This includes glycosidic linkage torsions, but also ring torsions, omega torsions, or NAc sidechain torsions.

GlyVicinity
generates statistics about the amino acids present in the vicinity of carbohydrate residues.

GlySeq
is dedicated to statistically analyse the sequences around glycosylation sites.


Notation related tools

LINUCS
(LInear Notation for Unique description of Carbohydrate Structure)
Converter from CarbBank style notation (2D representation) to LINUCS format.

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

SUgar MOtif search (sumo)
searches carbohydrate structures for motifs commonly used for carbohydrate classification, like N- and O-glycan cores, Lewis antigens, etc.


Tools to support MS / NMR analyses of glycans

GlycoFragment
The purpose of this application is to calculate and display the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS spectra.

Distance Mapping
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.

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