Docking of Ligand in a membrane protein

HADDOCK
1

Hi,

So I am working on a membrane protein and I want to understand how a particular ligand binds to the binding pocket. So, I want to first do a random search to find the residues which are interacting with the ligand.
In the web-server, for the final refinement step, I would like to use DMSO as the solvent. In that case, what should I keep the value for Eelec?

Also what would be the recommended number of models that I should generate initially?

I would be grateful for the help.

Thank you

2

Don’t change the dielectric.

And if using the 2.4 server make sure to then to include the solvent for the final refinement.

I would increase the sampling to 10000/400/400 - as explained on our protein-ligand tutorial:

https://www.bonvinlab.org/education/HADDOCK24/HADDOCK24-binding-sites/
3

Hi there, I am trying to assess if two proteins interact (docking a ligand on a surface receptor complex), but when I press the submit button, it does not register the job.

Can you please advice on this one?

Thank you

Y

4

Probably some validation error in your submission that prevents you to submit

At each stage check carefully all messages appearing on top!