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

From: David A Case <>
Date: Wed, 18 Aug 2021 08:28:25 -0400

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

...good luck...dac

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Received on Wed Aug 18 2021 - 05:30:03 PDT
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