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: ?

This PepSite web server can be accessed programmatically via a simple RESTful interface.

The match method

Currently, the only implemented method is match, which queries an input peptide sequence against a protein surface identified via a PDB/chain code.

It is also possible to specify the receptor protein using a UniProt ID or accession instead of a PDB code and chain identifier. PepSite will attempt to use the corresponding PDB structure with the best resolution. For more detail, see the help page.

parameter value example default
pdb 4-letter PDB code 1eak none
chain PDB chain id W none
uniprotid UniProt ID P53_HUMAN none
uniprotid UniProt accession P04637 none
ligand query peptide sequence GPAGPPGA none
format output format (see below) - html

Supported output formats

format decription
html web page with matches, scores, and molecular visualization
txt plain text output with list of matches and scores
pdb match coordinates in pdb format
rpdb coordinates of interacting receptor residues in pdb format
best_pval p-value of the best match in plain text


The following examples should be run from a Unix terminal after setting a variable with the base URL:


Predict binding of peptide sequence GPAGPPGA to protein from PDB 1eak, chain D, with returned as a plain text file:

curl -s "$url/match?pdb=1eak&chain=D&ligand=GPAGPPGA&format=txt" > result.txt

Retrieve only the p-value of the best match for the above example:

curl -s "$url/match?pdb=1eak&chain=D&ligand=GPAGPPGA&format=best_pval" > result.txt

Retrieve a PDB file with the top matches for the above example:

wget "$url/match?pdb=1eak&chain=D&ligand=GPAGPPGA&format=pdb" -O matches.pdb