Thank you Prof. D. Case.
I'll watch out for the points you have mentioned while going ahead with
this approach.
Best regards
On Wed, Jan 22, 2020 at 6:36 PM David Case <david.case.rutgers.edu> wrote:
> On Wed, Jan 22, 2020, Vaibhav Dixit wrote:
>
> >In a project, I am required to generate g-quadruplex structures for
> >sequences for which crystal structure data in not available.
> >Using amber tutorial B1 like procedure it is very easy to generate a
> >variety of normal DNA helix structures.
> >But I can't find a similar procedure for generating g-quadruplex structure
> >only from a sequence.
> >Thus I'm wondering if an expert on the list can suggest how can I approach
> >this requirement using AmberTools.
> >Will it make sense if I use an existing quadruplex PDB entry of identical
> >length and simply delete coordinates for the bases (keep
> sugar-coordinates)
> >and change residue names to required base e.g. DG to DA?
>
> I'd keep the N1/N9 atoms of the bases, and give it a try.
>
> Presumably(?), the guanine tetrads will be unchanged. However, there
> are lots of topological ways that the "connecting" bases can be
> arranged. Unless you know that your unknown structure has the same
> general arrangement as your input structure, you could generate a
> structure that is entirely wrong.
>
> ....dac
>
>
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--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
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Received on Wed Jan 22 2020 - 21:30:02 PST
