Doctoral dissertation
PURY: A Topology and geometry parameter library for small molecules
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Abstract
The number and variety of macromolecular structures in complexes with "hetero" ligands is growing. The
need for fast delivery of correct geometric parameters for their refinement, which is often crucial for
understanding the biological relevance of the structure, is growing correspondingly. The current standard
for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from
selection and analysis of crystal structures gathered in the Cambridge Structure Database (CSD). Clearly
such a manual approach cannot be applied to the vast and ever growing number of chemical compounds.
Therefore, a database, termed PURY, of geometric parameters of chemical compounds, together with a
server accessing it, has been developed. PURY is a compilation of the whole CSD. It contains lists of atom
classes and bonds connecting them, as well as angles, chirality, planarity and conformation parameters. The
current compilation is based on CSD 5.28 and contains 1978 atom classes, 32702 bonding, 237068 angle,
201860 dihedral and 64193 improper geometric restraints. Analysis has confirmed that the restraints from
the PURY database are suitable for use in macromolecular crystal structure refinement and should be of
value for the crystallographic community. The database can be accessed through the web server
"http://pury.ijs.si/", which from deposited co-ordinates creates topology and parameter files in forms for
refinement programs MAIN, CNS and RefMac. The server will, in the near future, move to the CCDC web
site.