Re: [AMBER] NAB input file containing first and second structure of RNA

From: David A Case <>
Date: Sun, 27 Nov 2016 16:06:55 -0500

On Sun, Nov 27, 2016, Mohaddeseh Habibzadeh wrote:

> The RNA sequence is the first structure in my mind, the secondary
> structure of RNA which is showing by parenthesis and dots ((..)) .
> I want to make a tertiary RNA structure (pseudoknot form) with my desire
> secondary structure.

OK: I sort of understand now. NAB doesn't include anyway to process secondary
structure designiations like '((..))'. I think you should explore other
possibilities (e.g. Rosetta), although the general problem of going from a
secondary structure description to 3D coordinates is very much an unsolved
problem. But NAB is not equipped to help very much with this: you could
expand the psedoknot code, but those are ideas from 20 years ago, and other
programs in that area have progressed a lot since then.


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Received on Sun Nov 27 2016 - 13:30:02 PST
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