Re: [AMBER] Regarding filling missing residues in a DNA strand

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Wed, 25 Aug 2021 10:43:58 -0400

Sruthi,
my colleague Vageli Coutsias develops a loop modeling code BRIKARD that I
believe he has applied to nucleic acids. I suggest contacting him directly
and maybe following up here if it works so that it's in the archive for
others to see.
evangelos.coutsias.stonybrook.edu

On Wed, Aug 25, 2021 at 8:59 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:

> The main problem is that the DNA is unwound in the central position but
> bound at the terminal positions. So some of the techniques are not easy. If
> someone could comment on some techniques, it would be really helpful
> Regards,
> Sruthi Sudhakar
>
>
> On Wed, Aug 18, 2021 at 5:58 PM David A Case <dacase.chem.rutgers.edu>
> wrote:
>
> > On Tue, Aug 17, 2021, Sruthi Sudhakar wrote:
> > >
> > >We are working on a DNA protein system and the crystal structure under
> > >consideration has around 5 missing residues in the DNA strand. The DNA
> > >duplex is in an unwound form, but we know what bases should be added in
> > >those places. Is there a methodology in NAB or directly in leap by which
> > we
> > >could fill those residues ?
> >
> > This is a hard problem, and neither NAB nor leap are likely to be of much
> > help. If the missing nucleotides are not at a chain terminus, filling in
> > missing ones is equivalent to a "loop building" exercise, which is
> > common for proteins and RNA, but less so for DNA. I didn't find anything
> > easily with a Google search, but maybe someone on the list will have
> > some thoughts on this. You could look at RNAmake, which attacks this
> sort
> > of problem for RNA: Joe Yesselman or others might have some thoughts
> about
> > using it for DNA.
> >
> > If you just need to add "unwound" DNA at the end off a chain, look for
> > articles (e.g. from the Lois Pollack group) about modeling
> single-stranded
> > DNA.
> >
> > ...good luck...dac
> >
> >
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Received on Wed Aug 25 2021 - 08:00:02 PDT
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