PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
- 1 June 1996
- journal article
- Published by Springer Nature in Journal of Computer-Aided Molecular Design
- Vol. 10 (3) , 255-262
- https://doi.org/10.1007/bf00355047
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.Keywords
This publication has 14 references indexed in Scilit:
- Expression, characterization and crystallographic analysis of telluromethionyl dihydrofolate reductaseActa Crystallographica Section D-Biological Crystallography, 1995
- Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural DatabaseJournal of Chemical Information and Computer Sciences, 1993
- Three-dimensional Structure of an Anti-steroid Fab′ and Progesterone-Fab′ ComplexJournal of Molecular Biology, 1993
- Automatic assignment of chemical connectivity to organic molecules in the Cambridge Structural DatabaseJournal of Chemical Information and Computer Sciences, 1992
- Determination of molecular topology and atomic hybridization states from heavy atom coordinatesJournal of Computational Chemistry, 1991
- Computer Simulation of Molecular Dynamics: Methodology, Applications, and Perspectives in ChemistryAngewandte Chemie International Edition in English, 1990
- SMILES. 3. DEPICT. Graphical depiction of chemical structuresJournal of Chemical Information and Computer Sciences, 1990
- SMILES. 2. Algorithm for generation of unique SMILES notationJournal of Chemical Information and Computer Sciences, 1989
- SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rulesJournal of Chemical Information and Computer Sciences, 1988
- The protein data bank: A computer-based archival file for macromolecular structuresJournal of Molecular Biology, 1977