can I obtain RosettaDock?
is available as part of the Rosetta++ package—see http://www.rosettacommons.org. It has been developed primarily on linux, but it also runs on windows and mac platforms.
like to recalculate the score for certain structures. Is there an easy way to do that
can score a pdb by running with the options
'-dock -score' and perhaps '-fullatom' for the
most-accurate all-atom score.
Note that I wouldn't compare scores between proteins with different
sequences. The scores are tuned to be relative to other
conformations of the same protein pairs.
- Do you
prefer the dock_mcm option or the more explicit
-dock_pert n p r for perturbation? I
noticed that in the example you have -dock_mcm.
- -dock_mcm determines the search protocol, and yes, this is the best option for that,
it means going through cycles of small perturbations, repacking, minimization. mcm=monte carlo minimization
-dock_pert specifies the start condition, that is, how is the starting structure
perturbed before beginning the whole search process. Using this
option and creating 1000 decoys means you are starting from a range of
positions near the input pdb position.
In the JMB paper fig 1a, -dock_pert is happing
in the pink box 'random start position', and ‘-dock_mcm'
turns on the 50x loop in fig 1b
in the example, -ex1 -ex34 are used. Why not -ex2 -ex3 as well?
is a bit of a scientific mystery at this point and probably arises from
our imperfect representation of side chain conformational ensemble through
rotamers. In testing, -ex2 improved the scores, but it improved
both native-like and false positive scores, making discrimination
harder. -ex34 = -ex3 and -ex4.
the scores between a protein and mutants of its interacting partner be
meaningful to compare? We have a bunch of mutants of a pair and
measured affinities. I remember a paper by T. Kortemme
& D Baker in PNAS, in which they used a very similar energy function
to find out binding energy hot spot. Basically I also would like to
do that for our sets of mutants.
could compare the RosettaDock scores, but the dock mode has not really
been tested or tuned to give information about mutants. It is
probably qualitatively ok, but I don't know how big the error bars are or
how large an energy is significant.
You can use Kortemme's technique directly
through the Robetta interface: http://robetta.org.
It is designed to analyze interface mutants.
We are currently working on projects to integrate these modes better.
Last update: 22 March 2006