Run PepSite on a PDB structure

PDB code:   PDB chain:  Use non-prot/hoh ats in surf calc?

Peptide sequence: ?

Run PepSite on your own PDB file

 Use non-prot/hoh ats in surf calc?

Peptide sequence: ?

Prediction of peptide binding sites on protein surfaces

Update July 2021 Various fixes have been made to account for: a) the age of this server (10 years) and b) changes to various things in the PDB data at There are remaining issues with PDB names, etc that are still rather broken. This is to do with new chain labelling in the PDB. If they are wrong/funny, do not worry: the right coordinate data are being used, but the names are not getting extracted properly.

Protein-peptide interactions are a vital part of many cellular signaling pathways (e.g., RTK signaling) and other cellular processes (e.g., endocytosis). A detailed view of such interactions enables a mechanistic description of how cell networks are regulated.

PepSite can predict binding of a given peptide onto a protein structure, enabling users to better understand the details of the interaction of interest. PepSite 2 is a complete rewrite of the original software and can generate results in seconds instead of minutes or even hours. (The original server is still available.)

When using PepSite 2, please cite:

PepSite: prediction of peptide-binding sites from protein surfaces.
Trabuco LG, Lise S, Petsalaki E, and Russell RB.
Nucleic Acids Res. 2012; 40(Web Server issue):W423-426.

Original PepSite reference:

Accurate prediction of peptide binding sites on protein surfaces.
Petsalaki E, Stark A, García-Urdiales E, and Russell RB.
PLoS Comput Biol. 2009 Mar;5(3):e1000335.