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recommended function type for cross links data

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recommended function type for cross links data


I want to use rosetta ab intio with constraints from cross links data that I have, what is the best function type to put in the constraints file? 

Furthermore, what is the best function type for co-evolution data (from GREMLIN)?



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Sun, 2018-08-05 06:57

Hi Merav,

I have a preprint version of a paper that discusses exactly that and may be published soon. You will also find references in there for previous attempts to use crosslinking data with Rosetta.

Check it out:


Mon, 2018-08-06 13:54

Generally speaking, the most common sorts of constraints you use in these situations are AtomPair constraints (often between the Calpha atoms) with FLAT_HARMONIC functions. This way you don't penalize things which are "in range", but apply a progressively steeper penalty as you go outside of the "allowed" region.

Regarding co-evolutionary data, take a look at papers from Ovchinnikov and Baker (e.g. to see dettails of how exactly they used this information.

Mon, 2018-08-20 11:51