Welcome To Pocket Creator

This tool allows you to create protein-ligand binding pockets with various sizes and shapes

Submit a protein and assign the ligand to create a binding pocket around it with your options

Please read the about page and click
on the Help » widgets for more information

Create a pocket:

Protein :

PDB id code :   View in PDB »

PDB file :

Ligand :

Automatically assign   Help »

Let the program assign the ligand automatically by selecting the biggest
selecting the biggest non-protein molecule in the complex

Assign by keyword :   Help »

If known, you can type the ligand's keyword.
for example :
RES367:A - will select residue RES, sequence number 367 in chain A
RES367:A,RES375:A - will select residues RES367:A and RES375:A only
RES367:A-RES375:A - will select all the residues between RES367:A and RES375:A

Pocket :

Size : Å radius  Help »

The radius in Angstroms to use as the maximum distance cutoff from the ligand
to the protein residues and other compounds in the protein database file

Shape : Induced Centered Cavitary   Help »

Induced - the pocket is selected by measuring the distance from each atom in
the ligand to each atom in the complex, so that the pocket will be "induced"
by the ligand's shape
Centered - the pocket is selected by measuring the distance from the geometric
center of the ligand to each atom in the complex
Cavitary - the pocket is selected by measuring the distance from the cavity
created in the binding pocket using the VOIDOO software (courtesy of
Dr. Gerard J. Kleywegt from Uppsala University)

More Options »

Replace gaps of up to : residues  Help »

The program looks for small gaps that are created between the saved
protein “strands” and fill them for up to the defined number of residues,
thus creating a smaller number of protein strands

Include :Ligand Water Molecules Atoms

Preserve structures :Helices Sheets

Terminals :None Adjacent Cα  Help »

The adjacent residue's C-alpha atom will be attached to each strand's
terminal that will be created

Last Update : June 7, 2006 | Copyright ©, 2006, The Hebrew University of Jerusalem. All Rights Reserved.