PRODRG, A PROGRAM FOR GENERATING MOLECULAR TOPOLOGIES AND UNIQUE MOLECULAR DESCRIPTORS FROM COORDINATES OF SMALL MOLECULES

A software package is described that operates on small molecules obser ved in the PDB collection of protein structures. Molecular topology fi les for many molecular modeling programs can be generated automaticall y. The three-dimensional coordinates of small molecules can be convert ed to molecular descriptor strings that encode them uniquely in order to enable small-molecule recognition, despite high variability in atom and molecule nomenclature. From this descriptor a plausible 3D struct ure can be regenerated using energy minimisation. Alternatively, an en semble of structures can be generated using a distance-geometry-based algorithm.