BALI: Automatic assignment of bond and atom types for protein ligands in the Brookhaven Protein Databank

A method for assigning hybridization states and bond orders to protein ligands from the Brookhaven Protein Databank(1) is presented. The assignment procedure is based on the recognition of simple chemical groups and on an analysis of bond length and bond angle data. Special care was taken on the proper handling of aromatic heterocyclic ring systems which are frequently found in small molecule ligands. Hybridization states and bond orders are assigned with a success rate significantly higher than what has been reported for previously published algorithms. The main application of BALI is to identify protein ligands in the Brookhaven Protein Databank and to add information about bond and atom types with a minimum amount of manual intervention.