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[ccp4bb] Stretching Modelled B-DNA - Programs
 

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CCP4bb <-- 2007 <-- April 2007 <-- 10 April 2007
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Subject: Stretching Modelled B-DNA - Programs
From: Balvinder Dhaliwal balvinder {- dot -} dhaliwal {- at -} GMAIL {- dot -} COM
Date: 2007-04-10
Dear CCP4bbers,

My original query was; "I am trying to find a program that enables the user
to vary the pitch of the generated output model of dsDNA.
I have found several programs that generate a dsDNA .pdb file given an
input sequence (random in my case), and a web server that allows 'curvature'
analysis of the output DNA
(http://hydra.icgeb.trieste.it/dna/).
However, I am unable to find a program that allows the pitch of the dsDNA to
be varied. I was wondering if such a program exists? And if so, where can it
be found?"

Thank you for the prompt replies. I was able to generate B-DNA models of
varying pitch.
Two of the more versatile tools for manipulating nucleic acid structures
are:-

i) NAMOT (suggested by William Scott, UCSC); download at
http://namot.lanl.gov/

ii) 3DNA (suggested by Nicola Abrescia, Strubi, Oxford); download at
http://rutchem.rutgers.edu/~xiangjun/3DNA/

Balvinder Dhaliwal.
(Baylor College of Medicine, Houston, Tx.)
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