PepSite

A structural method to predict peptide/protein binding
Evangelia Petsalaki, Alexander Stark, Eduardo Garcia Urdiales, Rob Russell


You can find more information on the following examples here.

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

Examples

1. 1i5h : RNEDD4 WWIII Domain from Rattus norvegicus

WW domains bind [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs.

If you give to pepsite as input the peptide sequence GTPPPNYDSL, the pdbid 1i5h and the chain id W you will get the result linked here.Don't forget to provide a title for the job. Providing an email might make it easier to track the job later.

2joc : RNEDD4 WWIII Domain from Rattus norvegicus
The PDB file with id 2joc is the equivalent unbound structure

If you give to pepsite as input the peptide sequence GTPPPNYDSL, the pdbid 2joc you will get the result linked here.Don't forget to provide a title for the job. Providing an email might make it easier to track the job later.

2. 1eak : CATALYTIC DOMAIN OF PROMMP-2 E404Q MUTANT from Homo sapiens


If you give to pepsite as input the peptide sequence GPAGPPGA, the pdbid 1eak and the chain id D you will get the result linked here. Don't forget to provide a title for the job. Providing an email might make it easier to track the job later.

1e88 : FRAGMENT OF THE GELATIN-BINDING DOMAIN OF HUMAN FIBRONECTIN
The PDB file with id 1e88 contains the gelatin binding fragment of fibrinectin without a peptide bound.

If you give to pepsite as input the peptide sequence GPAGPPGA, and the pdbid 1e88 you will get the result linked here. Don't forget to provide a title for the job. Providing an email might make it easier to track the job later.

3. 1w9h : PIWI PROTEIN FROM ARCHAEOGLOBUS FULGIDUS.


If you give to pepsite as input the peptide sequence PDNGTSAWGE, the pdbid 1w9h and the chain id A you will get the result linked here. Don't forget to provide a title for the job. Providing an email might make it easier to track the job later.