- automatic detection of sugar-like structures,
- determination and assignment of the correct sugar type based on its geometry and stereochemistry,
- recognition of glycosidic linkages and building of glycan chains, and
- generation of CHARMM inputs.
Please note that
- For proper identification of sugar residue names and their linkage information, carbohydrate atoms should be listed in HETATM with a chain ID and their connectivity information must be provided in PDB files. If the connectivity information is missing, one could generate it using PyMOL. PyMOL builds the CONECT table based on atom-atom distances , so make sure that all your bonds are correctly drawn (or see if unnecessary bonds are added).
- Glycan Reader is embedded in most other modules such as Solvator, Quick MD Simulator, Membrane Builder, etc.
- Chemical modifications of sugar residues are NOT provided at this moment; we are working on it.
- Glycan Reader supports all the options in PDB Reader.
- If you are not familiar with the first PDB reading step, please first watch these video demos.
- More glycan-related tools can be found in GlycanStructure.ORG.
References for Glycan Reader:
S. Jo, T. Kim, V.G. Iyer, and W. Im (2008)
CHARMM-GUI: A Web-based Graphical User Interface for CHARMM. J. Comput. Chem. 29:1859-1865
S. Jo, K.C. Song, H. Desaire, A.D. MacKerell, Jr., and W. Im (2011)
Glycan Reader: Automated Sugar Identification and Simulation Preparation for Carbohydrates and Glycoproteins. J. Comput. Chem. 32:3135-3141
S-J. Park, J. Lee, D.S. Patel, H. Ma, H.S. Lee, S. Jo, and W. Im (2017)
Glycan Reader is Improved to Recognize Most Sugar Types and Chemical Modifications in the Protein Data Bank. Bioinformatics 33:3051-3057