Hello!
I’m trying to dock a protein on a GPCR, that has of course a transmembrane domain. Since the protein I’m trying to dock should not bind the transmembrane domain i thought simply to restrain all the transmembrane domain as passive without the need to simulate any lipid membrane. Is this the correct approach?
You should rather define all solvent exposed parts as passive (or only one side if you know on which side it is binding)
And no need for explicit lipids.
If i don’t know the active residues of my proteins, would be possible to use haddock to perform “blind docking“? Is this the best strategy?
You can, but I would also try other servers, e.g. CLUSPRO and AlphaFold
And you don’t have any info about possible binding site for both proteins?
So I performed a run on AF3 Multimer, also adding 100 OLA (Oleic acids, to simulate a membrane), but the iPTM is 0.58, quite low. So I ran LightDock on the webserver and it worked, I was thinking to refine the ensemble on HADDOCK, following your nice tutorials, (LightDock+HADDOCK membrane proteins tutorial – Bonvin Lab). I do have a further question, in the tutorial the proteins are both made of a single polypeptide chains only so when you add the files in HADDOCK server you select the single chains from the .pdb files. Meanwhile my proteins, both the receptor and the ligand proteins, are made up of two chains, but how do I select that from the server? Because from the interface I am allowed to select one chain only per molecule that I upload. Any case thank you very much professor, I am reading much of the work of yours and Vangone as well, absolutely essential tools and very much easy to understand.
If you just want to refine the models, using the refinement interface of the server in which you upload directory the complex
It will detect the chains.