Member Site Forums Rosetta++ Rosetta++ – General docking search: first residue centroids, then full atom? Reply To: docking search: first residue centroids, then full atom?


    See the following answers from Docking developers.

    Dear Paul,

    If I understand correctly, you would like to dock two proteins, one of which is a yeast protein and the other is a kinase. I would go about it as follows:

    1. If some biological information is known like active sites etc which are known to be at the interacting interface, align the two molecules in a consistent manner. (Constraint files might be used to bias the simulations) (only -dock_pert 3 8 8 –spin flags are sufficient)

    2. If you have no idea about the interacting regions, it does not matter how the partners are aligned ( -randomize1 –randomize2 –dock_pert 5 10 10 –spin)

    3. If it’s only a dock_pert around 1000 decoys are sufficient whereas for a randomize run around 100k is a good number ( you might want a smart score filter)

    4. At the end look at the lowest scoring decoys. They are probably complex candidates. If on clustering the 200 lowest scoring decoys, a cluster of significant size with the representative member having one of the top (lowest) scores (subjective) is found, that is probably the best guess.

    A single low energy (good) point is not sufficient enough to be called a hit and might be a false positive.



    > 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.
    > Many thanks,
    > – Paul Shannon
    > Institute for Systems Biology