Small Molecule Binding Site Screening tutorial vs. Active residues determined experimentally


#1

I’m following the lower part of the Tutorial “Setting up a new docking run targeting the identified binding pocket”, however I have active residues defined by NMR chemical shift perturbations instead of ab initio docking; I’m entering those as Active Residues in the Molecule Definition menus and checking “Define passive residues automatically around the active residues”. Should I (1) as in the ab initio part of the tutorial, check the box in the Distance Restraints menu for ‘Define randomly ambiguous interaction restraints from accessible residues’?, (2) Set as in the ab initio part, in the Sampling parameters menu, Number of structures for rigid body docking -> 10000, Number of structures for semi-flexible refinement -> 400, Number of structures for the explicit solvent refinement -> 400, (3) NOT set in the Restraints energy constants menu” > Energy constants for ambiguous restraints menu, Last iteration (0-2) -> 0?

Thanks!


#2

Hello,

You should indeed NOT do (1) and (2) since those calculated restraints are incompatible with the manual active/passive residues you have added. They do not appear in the 2nd docking run protocol anyway. You might be mixing the two protocols there.
So you can apply (3), this will have the described effect, but applied to your restraints (any active/passive definition are ambiguous restraints). As explained at the beginning of the section Setting up a new docking run targeting the identified binding pocket this will allow to first target the binding site and make sure to draw the ligand in, then leave it enough freedom to explore several conformations.

But to stay inline with the protocol proposed, it would be maybe nicer to create, with the GenTBL interface, two sets of active/active and active/passive residues and apply them the same way. You can do it with your own active residues, as it is described in the tutorial (same section).

Hope this will help,

Mikael


#3

To add on top of what Mikael wrote:

  • using the GenTBL interface of HADDOCK, generate two files:
    • act-act.tbl with only active residues for both molecules 1 and 2 (no passive). All the residues that are the most shifted in your NMR CSP experiment should be listed as active and the ligand too.
    • act-pas.tbl where the ligand remains active but all the previously listed residues on the protein are now defined as passive.
  • following the tutorial, you will have to specify when to use each of the files. Pay attention to the step 6 and specify in the Restraints energy constants menu that the first file (act-act.tbl) must be used only in iteration 0 while the second one (act-pas.tbl) must be used in the iterations 1-2.

Please follow the tutorial step by step. You probably do not need to increase the sampling to 10000/400/400 if your CSP data are well defined enough.

Kind regards,
Adrien