Table 4.
Tools for prediction and analysis of carbohydrate/glycoprotein 3D structures.
| Name, Ref | Comment | URL |
| BALLDock/SLICK [92–93] | Protein–carbohydrate docking | |
| CARP [89] | Ramachandran plot-like analysis of glycosidic torsions | http://www.glycosciences.de/tools/carp/ |
| CAT | Conformational analysis tool, for analysis of MD trajectories | http://www.md-simulations.de/CAT/ |
| GLYCAM Biomolecules Builder [42] | Generation of glycan models and in silico glycosylation of proteins, preparation of input files for AMBER [94–95] | http://glycam.ccrc.uga.edu/ccrc/pages/3dspt.html |
| Glycan Reader [96] | Detection of carbohydrates in PDB files, preparation of input files for CHARMM [97] | http://www.charmm-gui.org/input/glycan |
| glyProt [98] | in silico glycosylation of proteins | http://www.glycosciences.de/modeling/glyprot/ |
| glyTorsion [89] | Statistics of torsion angles of carbohydrate structures in the PDB | http://www.glycosciences.de/tools/glytorsion/ |
| glyVicinity [89] | Amino acids in the spatial vicinity of carbohydrates in the PDB | http://www.glycosciences.de/tools/glyvicinity/ |
| pdb2linucs [85] | Detection of carbohydrates in PDB files | http://www.glycosciences.de/tools/pdb2linucs/ |
| pdb-care [88] | Validation of carbohydrate 3D structure files | http://www.glycosciences.de/tools/pdbcare/ |
| Sweet-II [39] | Prediction of carbohydrate 3D structures | http://www.glycosciences.de/modeling/sweet2/ |