I am a novice, learning RosettaDock by trial, error, and reading the web.
My goal is to dock a yeast protein to a kinase -- we have other experimental evidence
that the protein in question is a direct substrate of that kinase. I hope that docking can
either contradict, or lend support, to that claim.
My question: how do I locate the 'funnel'?
My naive approach has been to
1) run hundreds of simple fast searches, with side chains expressed only
as residue centroids
2) find some low-scoring results
3) run those again in full-atom mode (are the full-atom scores still good?)
4) eventually, use the lowest scoring full-atom models for docking in
perturbation mode, hoping to find a funnel
Does this make sense? Or does 'residue centroid' docking mode leave out
too much detail to be useful? Finally, is there a guide for all of this? I have
not found one.
- Paul Shannon
Institute for Systems Biology