A complete small molecule dataset from the protein data bank

A complete set of 6300 small molecule ligands was extracted from the protein data bank, and deposited online in PubChem as data source ‘SMID’. This set’s major improvement over prior methods is the inclusion of cyclic polypeptides and branched polysaccharides, including an unambiguous nomenclature, in addition to normal monomeric ligands. Only the best available example of each ligand structure is retained, and an additional dataset is maintained containing co-ordinates for all examples of each structure. Attempts are made to correct ambiguous atomic elements and other common errors, and a perception algorithm was used to determine bond order and aromaticity when no other information was available.