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Updated: Jun 12, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
Published on: July 8, 2025
PESDserv: a server for high-throughput comparison of protein binding site surfaces
Sourav Das1, Michael P Krein, Curt M Breneman
1Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, NY 12180, USA.
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/
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