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Re: [modeller_usage] Fwd: Modelling protein of interest with RNA



On 9/6/17 9:33 PM, Saravanan Parameswaran wrote:
First,​ the RNA structure is disordered in the model.

Modeller doesn't model RNA - it'll just copy it from the template to the model (you should use the '.' residue type in both the template and model sequences). You *can* use 1-letter codes for each nucleic acid, but Modeller won't use any information from the template - you'll have to provide your own restraints. Otherwise, the nucleic acids will just flop around without restraints, likely what is giving you a disordered structure.

​Second, a nucleotide is modified (ARA) in the bound RNA with my protein of interest. I want to model it as such, not ligand. I want it to be a modified nucleotide since, modelling it as ligand may bread the RNA strand.

See https://salilab.org/modeller/FAQ.html#8

You will again need to impose a suitable set of restraints on this residue, which is not an easy task.

	Ben Webb, Modeller Caretaker
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             https://salilab.org/modeller/
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