Run PepSite on a PDB structure

PDB code:   PDB chain:

Peptide sequence: ?

Run PepSite on your own PDB file

Peptide sequence: ?

You have predicted binding of the peptide GPAGPPGA on the protein surface from PDB 1eak, chain D (72 kDa type IV collagenase from Homo sapiens).

The interactive visualization below shows the protein structure and a predicted peptide binding spot. (Don't see anything?) To learn the basic controls, click here.

To display a different prediction, click on the correponding row from the table below, which shows the top matches ranked according to statistical significance (p-value).

rank p-value N
1 0.01766 4 ----- pro-2 ala-3 ----- ----- ----- gly-7 ala-8
2 0.02011 3 ----- ----- ala-3 ----- pro-5 pro-6 ----- -----
3 0.02011 3 ----- ----- ----- ----- pro-5 pro-6 ----- ala-8
4 0.02233 4 ----- pro-2 ala-3 ----- ----- ----- gly-7 ala-8
5 0.03359 3 ----- ----- ala-3 ----- pro-5 pro-6 ----- -----
6 0.03359 3 ----- ----- ----- ----- pro-5 pro-6 ----- ala-8
7 0.04668 3 gly-1 pro-2 ala-3 ----- ----- ----- ----- -----
8 0.06629 3 ----- ----- ala-3 ----- pro-5 pro-6 ----- -----
9 0.06629 3 ----- ----- ----- ----- pro-5 pro-6 ----- ala-8
10 0.07094 3 gly-1 pro-2 ala-3 ----- ----- ----- ----- -----

Each row from the table above is colored according to statistical significance (p-value) following the color scale below (red = highly significant; yellow = moderately significant; white = not significant).

You can download a PDB file with the top matches or with the interacting receptor residues. For a description of the format used, click here.