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.
- 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.
- 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?
- 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