Glycan Reader has been integrated into the CHARMM-GUI web interface.19 (link) The user can either specify the PDB ID or upload the PDB structure into the server to generate the carbohydrate or protein/carbohydrate complex structure. If a carbohydrate is detected, then the graphical representation of the carbohydrate chain sequence will be displayed and the user can select the carbohydrate chains that they want to initialize in CHARMM (see Fig. 4 ). CHARMM allows modification in chemical structures, e.g., disulfide bond formation or phosphorylation using patch residues, and glycosidic linkages are generated using specific patch residues in CHARMM. The Glycan Reader web interface assigns the proper patches for glycosidic linkages and generates the CHARMM protein structure file (PSF) and coordinate files in both the PDB format and the CHARMM-specific coordinate format (CRD).
Currently, there are various patch residues available in the CHARMM carbohydrate force field to cover a range of carbohydrates including the majority found in eukaryotes.25 For example, O-methyl-, octyl-, dodecyl-, phosphate, and sulfate groups can be added to the reducing end of a sugar, and those modifications are properly patched in the PSF generation step (seeTable 2 for the complete list of patch residues available). However, other types of common derivatizations, such as deoxidation, are not available, and, in such cases, the basic form of the carbohydrate molecule is used without modification and Glycan Reader informs the user. For example, if a user uploaded a structure of 2-deoxy glucose, a glucose molecule will be generated instead.
Currently, there are various patch residues available in the CHARMM carbohydrate force field to cover a range of carbohydrates including the majority found in eukaryotes.25 For example, O-methyl-, octyl-, dodecyl-, phosphate, and sulfate groups can be added to the reducing end of a sugar, and those modifications are properly patched in the PSF generation step (see