Attraction and Repulsion Tutorial
If you have experimental information that indicates certain residues are involved in binding or remain surface accessible during binding,
you can influence the results of the docking by setting attraction or repulsion on these residues.
- To access the ability to specify constraints, you will need to click on "Advanced Options" and then "Attraction and Repulsion". You should then see
the entry fields for attraction and repulsion.
- To specify attraction, enter the residues that you believe participate in the binding in the format of "chain-residue". In the example below, we have
chosen to turn on attraction for residues 27 and 34 of chain C in the receptor and residue 65 in chain B and residue 68 in chain E of the ligand.
- Repulsion can be specified similarly, but we also provide the option for you to upload a pdb file containing the residues you would like to mask.
You may switch between these modes by clicking on "Use PDB Masking File".
- To generate a PDB masking file, we recommend using Pymol. When you open your file, you will want to find the button marked
with "S" in the lower right corner to see the sequence of your protein.
- After clicking on the S, you will now see the sequence of your protein at the top of the window. You can then select residues by clicking on the letters.
This will create an selection object called "sele" on the right side of your screen that holds these residues. You can also see the selection by what residues
have dots placed on them in the viewer.
- You can then choose File->Save Molecule from the menu. This will give you a window where you choose to save "sele". You can then upload this pdb file as
your masking file.
If you have any questions, please look to see if it is addressed on the help page. If you have any suggestions, please