docking site in pymol

Question

[elmira b]

Hello,

I used Cluspro, a protein-protein docking server, to identify docking site between two proteins. Now I have a pdb file of two interacting proteins. I wonder which steps I should take to visualize the interaction site between these proteins and measure distance between their amino acid in Pymol? My knowledge about Pymol is very basic.

Thanks,
Elmira

Answer 1

[glihm]

Hi Elmira,

If you have, from the docking program, the pdb files and proteins correctly arranged, you have this script which helps you to visualize interactions site between two proteins.

Then, in Pymol you can easily measure the distance between Atoms / AminoAcids / Objetcs with the command line OR Gui.

Gui paths : From the menu, select the Mouse wizard, and you will have "Distance". Then, you have to click on the two amino acids to compare.

I hope this will be helpful!