Hi, I've a question about protein docking with constraits.
i want to run a low resolution docking of 2 proteins each around 450 residues to understand how the dimer is being formed based on distances from cross-linking experiment.
I have got around 300 distances that i want to use as constraints, i know that all of them cannot be satisfied at the same time, giving rise to multiple binding modes. So i really hope to find some poses that will satisfy max amount of my cross-link distances. Moreover all of them come with kind of confidence scores. For example (first column=first residue; second=second residue; the distance is not fixed but should be <25A; the last column is the confidence= rosetta should use it as a weight thus to give a preference to the ones with bigger number):
Reading the threads, i found out about the possibility to use AmbiguousConstraints.
AtomPairConstraint Atom1 Res1 Atom2 Res2 BOUNDED lb ub sd rswitch Experimental_constraint
AtomPairConstraint Atom1 Res1 Atom2 Res2 CONSTANTFUNC value
Do you think it's a good idea to have 300 ambiguous constraints?
Can anyone point me out the way to do it?
I would really like some more information about constraints with weights.
So far i just obtained prepacked version of my protein (the solved structure i am using is a dimer, and thus i am trying to find out alternative dimer forms of this protein based on cross-linking experiment).
Thanks so very much !