Subject: Re: [modeller_usage] DNA nucleotide modeling
From: Modeller Caretaker <>
Date: Mon, 4 Oct 2021 10:16:08 -0700
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