Subject: Summary: Software for DNA helix analysis

From: "Hans De Winter" <[email-masked]>
Date: Tue, 11 Jun 1996 15:51:04 -0600

Hi All:-

About a week ago I posted a question regarding software for the analysis
of oligonucleotide structure in terms of twist, roll, and so on.
Here is a summary of replies (shortened). Thanks to all who replied.

Hans De Winter

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NEWHELIX: It can be found on our departmental server at www.mbi.ucla.edu.

Ho Leung Ng ([email-masked])

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You might like to see the helix computational methods in :

Computers and Chemistry, (1996) vol. 20, pp. 339-345.

James Crabbe ([email-masked])

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Richard Lavery and Heinz Sklenar have written a very useful nucleic acid
helical analysis program called CURVES. I think the current version is CURVES
4.1 and its available free directly from the author:

| Richard Lavery                        | Tel  : +33 1 43 25 26 09  |
| Laboratoire de Biochimie Theorique    | Fax  : +33 1 43 29 56 45  |
| Institut de Biologie Physico-Chimique |                           |
| 13, rue Pierre et Marie Curie         | Email: [email-masked]    |
| 75005 Paris, France                   |                           |

Alexander Hillisch ([email-masked])

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Hei Hans,

I use a program called CURVES for this purpose. CURVES allows (optional)
a bending of the helix axis whereas NEWHELIX only handles a rigid
helix axis. But the differences for roll, twist etc. are small.
CURVES is available from Richard Lavery in Paris.

Newhelix is now available within Insight from Biosym/MSI.
Hope it helps,

Peter ([email-masked])

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Please contact either Prof. Wilma Olson at [email-masked] or Dr. Marla
Babcock at [email-masked].  They have a program (the name of which
escapes me at the moment) which is superior to NEWHELIX.

References for their program are:

J. Biomol. Struc. Dyn. vol 11, no.3 pp 597-628 (1993)
J. Mol. Biol. vol 237, pp 98-124 (1994)
J. Mol. Biol. vol 237, pp 125-156 (1994)

Jeff Nauss ([email-masked])

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See amber41/Questions/0Net/programs.anal or the same
file under 'info from the net' on our web site

  http://www.amber.ucsf.edu/amber/

Bill Ross ([email-masked])