New opportunities for protease ligand-binding site comparisons using SitesBase.

The rapid expansion of structural information for protein ligand-binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross-reactivity and toxicity. We have developed SitesBase, a comprehensive database of ligand-binding sites extracted automatically from the Macromolecular Structure Database. SitesBase is an easily accessible database which is simple to use and holds pre-calculated information about structural similarities between known ligand-binding sites. These similarities are presented to the wider community enabling binding-site comparisons for therapeutically interesting protein families, such as the proteases and for new proteins to enable the discovery of interesting new structure-function relationships. The database is available from http://www.modelling.leeds.ac.uk/sb/.