Hi Cristina,
thank you so much!
This is a great idea!
giulia
2016-04-19 11:56 GMT-07:00 Christina Bergonzo <cbergonzo.gmail.com>:
> Hi,
>
> In addition to what Dave mentioned, you could build a duplex and use
> targeted MD to flip a base out of the helix.
> I would recommend using this reaction coordinate:
> http://pubs.acs.org/doi/pdf/10.1021/ct9001575
>
> -Christina
>
> On Tue, Apr 19, 2016 at 12:24 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Tue, Apr 19, 2016, giulia palermo wrote:
>> >
>> > I am trying to build a double stranded DNA with Nucleic acid builder
>> > including an EXTRUDED guanine.
>> > Is it possible to do it with NAB?
>>
>> It would not be easy with the building capabilities in NAB. I'd suggest
>> finding an example of an extruded guanine in the PDB, and use that
>> fragment to
>> build what you want. The frames capability in NAB might be helpful, or you
>> might just want to do it interactively in a visualization program.
>>
>> ...dac
>>
>>
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>
>
>
> --
> ---------------------------------------------------------------------------------------
> Christina Bergonzo, PhD
> Postdoctoral Researcher
> Department of Medicinal Chemistry, University of Utah
> http://home.chpc.utah.edu/~cheatham/
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Received on Tue Apr 19 2016 - 14:00:03 PDT
