Problem: Induced fit in ensemble homo-dimer docking of an IDP.
I have an ensemble of over one hundered monomeric conformations of a particular IDP. I am interested in creating dimeric states from the monomer ensemble by cross docking. RosettaDock 4 is well suited for low resolution docking due to its adaptive conformer sampling (ACS) feature which imitates conformation selection. However when it comes to high resolution refinement, RosettaDock 4 only refines the interface residues (the same is true with SymDock). A recent paper (SymDock2) implements all-atomic full protein backbone induced fit mechanism after low resolution docking for symmetric complexes (Roy Burman, S. S., Yovanno, R. A. & Gray, J. J. Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes. Structure 27, 1041-1051.e8 (2019)).
Considering that I have to dock vastly different conformations of an IDP, I want to consider this problem as docking heteromers. So I do not want to use SymDock2 but at the same time have a tighter fit by using the full-backbone induced-fit protocol in SymDock2. I also cannot use RosettaDock 4 as it is not have a full induced fit protocol for high resolution refinement. I am wondering if I can use the high resolution refinement protocol in SymDock2 in such a way that the conditions for symmetry can be relaxed?
The low resolution docking which imitates conformation selection is straightforward in its implementation using RosettaDock 4. The problem is with high resolution refinement of these structures. Do I need to create a new xml script to implement this or is there a way to smartly circumvent this in SymDock2 ? Can I take a RosettaDock 4 xml script and change the mover part for the high resolution refinement in such a way that the entire backbone undergoes an induced fit binding.
Any inputs will be appreciated.
The induced fit in SymDock2 was only meant to resolve minor clashes. It is essentially a low cycle fastrelax. So you might be better off relaxing the complex you get from RosttaDock4 instead of trying to employ SymDock. SymDock or any symmetric protocol in Rosetta requires the creation of a symmtery definition as per which the pose is symmetrized. Docking with RosettaDock4 does not guarantee a symmetric pose, in fact it won't be symmetric most of the time.
None of these protocols have been tested on IDPs or extremely flexible regions, so it is difficult to predict the scientific accuracy of any model that you obtain.
Hope that helps.
Thanks for the explaination. If I am correct, this is achieved by ramping the vdW replusive term.