hellow, i wish to know whether modeller can be used as a general optimization tool. I have a structure of my protein... also know its binding site to another protein (its a protein-protein complex). i just want to apply simulated annealing to the binding site of my model, to find the best binding conformation... can modeller do that for me??
regarding the same, please apprise me of some details...
firstly, do i need to use the restraints generated by modeller... if yes, which ones??
secondly, what new restraints, if at all, should be applied(as a part of special restraints).
thirdly,is it necessary to use homology basis, the alignment, templates, and homology derived restraints...??
if anyone could give me a sample top script as to how the problem can be tackled, it would be a great help... moreover, any other nuances/suggestions in the approach would be appreciated...
thanks very much,
sincerely, himanshu