To annotate glycans in a given PDB file, Glycan Reader uses an algorithm that can detect carbohydrate-like molecules and assign correct carbohydrate types based on their molecular topology and 3D structures. The overall scheme in Glycan Reader is shown in Figure 1 and illustrated in Figure 2. Molecular topologies are built based on the HETATM records and CONECT records in a PDB file, and molecules that do not have carbohydrate-like topology are not considered. The chemical groups that are attached to the carbohydrate-like molecules are then examined to assign the correct carbohydrate type. Once the monomeric units are identified, glycosidic linkage types are determined.