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radius of gyration as constrain

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radius of gyration as constrain


I am trying to model missing C terminus of my protein using FloppyTail. I have experimental data regarding the radius of gyration that I want to use as constrain to narrow down the search space. How can I put that constrain?


Thank you


Post Situation: 
Sat, 2018-05-05 23:00

I'm not aware of a method for importing radius of gyration data into Rosetta.  

Rosetta has a generic radius of gyration term defined, but I do not beleive it lets the user set a specific radius.  It's intended for ab initio folding so it just favor small radii over large ones.  I don't know if the term is functional on fullatom poses (it may only work in centroid).  I could assist you in activating it in FloppyTail - it would probably at least work in the centroid phase.

I can tell you from experience that Rosetta's scorefunction wants to make things relatively stuck together even in the absence of an explicit radius of gyration term.  FloppyTail's lowest scoring models will tend to have any flexible regions stuck together or stuck against larger protein bodies; it's rare for the best models to have much protein out loose in space.  This may mean that just running it as-is and comparing to your RG data after the fact as a model filter may be sufficient.

Mon, 2018-05-07 11:42