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


BACKGROUND
The server is freely accessible at http://reccr.chem.rpi.edu/Software/pesdserv/
Das
Sourav
S
Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180, USA.
Krein
Michael P
MP
Breneman
Curt M
CM
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D030562:Databases, Protein; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software
D008024:Ligands; D011506:Proteins