Rigidity, cluster size and RMSD during multi-body docking using Haddock 2.4

I am performing protein-DNA docking using the multi-body interface.
I am providing a protein-DNA complex (a previously docked structure from Haddock) as one of the molecule, and PDB structures of two other peptides as the second and third molecules. As I want to maintain the same interactions for my protein-DNA complex I am making it rigid in the semi-flexibility option. But the docked results show that the interactions between the protein DNA complex have changed.

  1. Is it possible to make the protein-DNA complex completely rigid so that I get the same interactions even after it is allowed to dock with the other two peptides.
  2. The docked results show only a single model in each cluster (total of 400 structures) meaning the cluster size is low. Does a low cluster size indicate that the docking pose is not very good?
  3. The RMSD value is around 44. Is that a good value and is there any criterion for selecting good rmsd value in haddock.

Thanks in advance
K Sindhu

You basically have no clustering since the size of each cluster is 1. Which means your run is not converging. Also for multibody docking rather use FCC clustering.

What kind of info do you have to target your peptides on the protein-DNA complex?

What kind of changes do you see within the protein-DNA complex?

Dear Bonvin,
Thank you for the reply.
I see that my protein molecule is being shifted from its position from the 3’ to 5’ end of DNA. I find a decrease in non bonded contacts made with the 3’ end of DNA and increase in H bonds and non bonded contacts towards the 5’ DNA.
I want my protein to remain in contact with DNA with the same bonds which I give as input so that I can clearly view how the other protein molecules given in the multi-body docking run will behave with the protein-DNA complex.

K Sindhu

You probably have to better define your interfaces. When docking to DNA, the ends should usually be excluded from the list of active/passive for example to avoid end effects/artefacts.

Are you inputting a Protein-DNA complex as one molecule?

Molecule 1: Protein-DNA
Molecule 1: Protein
Molecule 2: DNA

I am giving protein-DNA as one molecule.
Molecule 1: Protein-DNA

If this is the case, your protein-dna complex does not move. Try double checking the numbering of your residues/bases.

When I gave a protein-DNA complex as one molecule and made it rigid I expected that there would be no changes in bonds within the protein-DNA complex. I have rechecked and found the number of bonds decreases and the corresponding residues involved changes. Without giving any restraints is it possible to make sure that I can get the same bonds.
I have another question as well. Can you help me solve:
When the protein-DNA complex is given to dock with another protein as molecule 2 and semi-flexibility set as default (automatic) for both, the protein in the protein-DNA complex completely changes its position with respect to DNA, moving from 5’ to 3’ end. What I understand is that the protein-DNA will be considered as a single body and is passed through rigid body docking. During semi-flexible only particular interfaces from rigid body docking are made flexible. In that case how is my protein in the protein-DNA complex completely moving from one end of the DNA to the other?

Thanks in advance
K Sindhu

Can you share a run with us so that we can take a look?

Also what do you mean exactly by “bonds”?

By ’ bonds’ I mean interactions between the two molecules. After analysis of the docked structures obtained through Haddock I find that some interactions are H bonded. Some others are non-bonded, I am sorry to use the common term ‘bond’ they are the interactions between the two molecules.
I am attaching herewith a run file of the condition where I have given a protein-DNA complex (protein bound to DNA at 5’ end) as molecule 1 and another protein as molecule 2. However the results show that the protein in protein-DNA complex shifted to 3’end.

parameters BRCT(5’)+RING.txt (387 KB)

I suggest to try the 2.4 web server.

It could well be that in the 2.2 server, when one molecule is a protein-DNA complex the server does not automatically define restraints between those to keep the conformation as is.

Note that you can always define additional distance restraints to keep the complex together. Upload those as unambiguous restraints (Expert level required).