Re: [modeller_usage] DNA nucleotide modeling

[Modeller Caretaker <modeller-care@ucsf.edu>]

On 9/29/21 4:28 PM, Rana Rehan Khalid wrote:
> I have a nucleotide Adenine (please see figure) I want to model it on 
> the particular atomic position of DNA, can I do it in the modeler. I 
> mean can the modeler generate the model in which I have both input 
> files. Please guide me if any ideas thanks.

Modeller does comparative modeling of proteins, i.e. amino acids, not 
nucleic acids. Although if you have DNA/RNA in your template structure, 
Modeller can copy it from template to model and restrain it to preserve 
any protein contacts, just like any other ligand. See 
https://salilab.org/modeller/10.1/manual/node18.html

	Ben Webb, Modeller Caretaker
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