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Protein-Protein Docking

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Protein-Protein Docking

In trying to understand the numerous rosetta options I wanted to see if anyone could give some guidance on how to go about the following.

I have two proteins A and B that I need to dock where the interface between the two proteins is known from sequence homology of an already solved PDB structure for proteins C and B.

On Protein A I can do the low resolution model with the appropriate constraints and then do the high resolution docking. When the high resolution model is constructed I am under the assumption that the backbone of Protein A will not be adjusted. Once I have a high resolution docking model of Protein A and Protein B is there a particular Rosetta process that can be used to see how the docking would change the overall structure of Protein A. On another interface of Protein A it has a couple loops that could change/move based on docking with Protein B. Not sure how to have Rosetta explore finding a model with overall minimal energy where loops or other regions Protein A may change based on the docking.

Fri, 2009-08-07 01:31

None of the currently released executables will do flexible-loop docking, so far as I know. There is a set of flags that will do this in rosetta++; I do not know what they are.

You may have some luck with the DockDesignParser. If (this is a big if) it allows loop modeling, you can tell it to cycle between docking and loop modeling. I'm not sure if it does or not.

Fri, 2009-08-07 15:54