PESDserv: a server for high-throughput comparison of protein binding site surfaces.

SUMMARY: Structure-based approaches complement ligand-based approaches for lead-discovery and cross-reactivity prediction. We present to the scientific community a web server for comparing the surface of a ligand bound site of a protein against a ligand bound site surface database of 106 796 sites. The web server implements the property encoded shape distributions (PESD) algorithm for surface comparison. A typical virtual screen takes 5 min to complete. The output provides a ranked list of sites (by site similarity), hyperlinked to the corresponding entries in the PDB and PDBeChem databases. AVAILABILITY: The server is freely accessible at http://reccr.chem.rpi.edu/Software/pesdserv/