title: PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules.
abstract: A software package is described that operates on small molecules observed in the PDB collection of protein structures. Molecular topology files for many molecular modeling programs can be generated automatically. The three-dimensional coordinates of small molecules can be converted 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 structure can be regenerated using energy minimisation. Alternatively, an ensemble of structures can be generated using a distance-geometry-based algorithm.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Leeds, UK.
authors.forename: D M
authors.initials: DM
authors.lastname: van Aalten
authors.forename: R
authors.initials: R
authors.lastname: Bywater
authors.forename: J B
authors.initials: JB
authors.lastname: Findlay
authors.forename: M
authors.initials: M
authors.lastname: Hendlich
authors.forename: R W
authors.initials: RW
authors.lastname: Hooft
authors.forename: G
authors.initials: G
authors.lastname: Vriend
mesh_terms: D008024:Ligands; D008358:Mannose / Q000737:chemistry; D008727:Methotrexate / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D019301:Oleic Acid / Q000737:chemistry; D011374:Progesterone / Q000737:chemistry; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins; D019301:Oleic Acid; D011374:Progesterone; D008358:Mannose; D008727:Methotrexate