Hello everyone,
I used HDOCK to model the homodimeric form of a protein. I want to refine the docking solutions using the protocol briefly described in the paper below:
Article Evaluation of Predicted Protein–Protein Complexes by Binding...
The authors used Amber for energy minimization and MD simulation employing the GB implicit solvent model. After energy minimization and heating steps, the authors did use restraints to avoid dissociation due to possible initial sterical overlap and to improve the sterical complementarity at the interface.
I want to know which tools from AmberTools I should use to apply the following restrictions in the production run:
- small distance restraint (force constant 0.5 kcal/mol.Angstron²) between the center of mass of ligand and receptor [in my case, the two subunits of the homodimer];
- weak distance restraints between the C-alpha atoms at the interface of the proteins to push the binding partners toward each other (force constant 0.25 kcal/mol.Angstron²).
A) Distance restraint between the center of mass of the first subunit and the center of mass of the second subunit.
B) Positional restraint applied separately to the center of mass or geometrical center or initial coordinates of each subunit.
The magnitude of the force constant is system-dependent: it should be high enough to prevent dissociation but not unnecessarily too high.
Martin Klvana, I am grateful for your answer to my question.
Since I posted the question yesterday I've seen in Amber's manual that it's possible to create a RST file with some complicated types of constraints that let you set the center of mass. I was already working on this, defining the center of mass of each subunit using the C-alpha atoms of each residue at the interface. Thanks to your answer I think I'm on the right track.
Thank you again.
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