Re: [AMBER] How to create a model of a G-Quadruplex and imotif structure using the sequence information

From: David A Case <>
Date: Mon, 28 Jun 2021 08:31:22 -0400

On Fri, Jun 25, 2021, Ramanathan Rajesh wrote:

>In our group, many G quadruplex and imotif sequences were purchased and
>various studies were conducted using some synthesized ligands. We would
>like to substantiate these results through molecular dynamics and we use
>AMBER18. The crystal structures of some of these sequences are not
>available. IN such scenarios is it possible to create such systems using
>Leap/NAB module just from the sequence information?

I don't think NAB would be very good for such a project. There is a wide
variety of ways (even topologies) for how the loops connect the core
quadruplex structure.

You might search on something like 'g-quadruplex structure prediction',
although I didn't see any obvious hits in a cursory look.


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Received on Mon Jun 28 2021 - 06:00:03 PDT
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