Protein+Ligand docking using HADDOCK webserver

HADDOCK
1

​
Dear All,

I am super new to HADDOCKING!!! through tutorial I understood on how to perform docking involving two proteins but I have a specific case where I couldn’t understood everything. So I posting my question to get few feedbacks.

I have to dock a protein + peptide(where one of the Cysteine residue is MTSL spin labelled).
I have a pdb for a receptor, for peptide I dont have pdb, so I created using coordinates using XPLOR(where there is an option to for CYSP(Cys with MTSL spin label)).

My question are,

  1. DO I have to prepare the pdb (peptide+MTSL) in HADDOCK format, i.e nomenclature of HADDOCK “CYM” residue is same as “CYSP” residue of XPLOR/CNS. I didnt find a “CYM” pdb to compare with CYSP pdb.

  2. Which interface would be suitable to run receptor+peptide-MTSL docking, I am asking because initially I am going to use only CSP data from NMR followed by I want to use distance restraints from PRE data. Again I can only input AIR for receptor and for peptide we have any restraints. In this scenario should I leave the restraints option black?

  3. In another case, I have to dock a protein with a ligand(organic) I have again created a topology and parameter file for this ligand using http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg, again the topology and parameter for ligand is in CNS format. Therefore for protein+ligand docking do I have to use guru interface? Is there is a option to upload my topology and parameter file in to HADDOCK.

I would highly appreciate your comments, suggestions,

Have good weekend…

With many thank…
Vince

2

  1. Yes - simply change the residue name to CYM - missing atoms will be automatically generated

  2. Easy as a start should work, although you might want to follow our protein-peptide docking protocol See for example the following tutorial:

http://www.bonvinlab.org/education/molmod/docking

The peptide should be defined as passive (again see the tutorial)

I would suggest however to possibly start modelling without the MTSL tag. It only complicate things (and is also kind of sticky…)

  1. The HADDOCK server will generate automatically PRODRG parameters. Make sure your ligand is defined as HETATM. No need to upload parameters. See for protein-ligand docking the following tutorial:
3

Dear Dr. Bonvin,

Thank you so much for your kind reply with precise information to run docking of receptor and a peptide with MTSL tag on.

I will also run receptor and peptide=MTSL docking without MTSL tag on. For this run I will consider CYS instead of CYM.

Thank you so much…
With many thanks…
Vince