recommended function type for cross links data

[Anonymous]

Hi,

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)?

Thanks,

Merav 

[Anonymous]

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: https://doi.org/10.26434/chemrxiv.6030563.v1

Állan.

[Anonymous]

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. https://www.ncbi.nlm.nih.gov/pubmed/28104891) to see dettails of how exactly they used this information.

[Author]

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