Subject: Summary on DNA structure analysis software.

From: K Bryson <[email-masked]>
Date: Fri, 10 Dec 1993 12:01:05 +0000 (GMT)

Hi,
		this is a summary of my findings on Nucleic Acid
	structure analysis software ...

	Original Posting
	----------------

> 	Hi,
> 		A previous message on a database for Nucleic Acid
> 	X-ray structures has got me wondering about how much software
> 	is out there to analyse nucleic acid structures.
> 		I know of R.E. Dickerson's Newhelix93 program for static
> 	structure analysis but do not know any other programs for the
> 	analysis of features not provided by this program such as
> 	Shear and Opening Parameters between base-pairs.
> 		For trajectory analysis I know G. Ravishanker has a
> 	program called 'Curves, Dials and Windows' and R. Lavery has
> 	a program called CURVES 3.0 ( not sure if it's the same program ),
> 	but I do not have sources or know the availability of these.
> 
> 		I would be grateful to receive information on these types
> 	of packages, personal feelings about their use, and sources to 
> 	obtain them.
> 		If the response is fruitful then I will form a summary of
> 	programs, their features and ftp sites.
> 
> 	Thanks,
> 		Kevin.

>From [email-masked]
----------------------------

For my dissertation work, I analyzed DNA structure in terms of individual 
base pairs.  To describe the orientation of any two bases (base paired 
or not) I used three translations and three rotations from a transformation 
matrix.  Furthermore, my algorithm was reversable to allow building of 
DNA polymers (and RNA for that matter) from the translation and rotation 
parameters.  The publication of the paper has been delayed for numerous 
reasons ......  You could also look up my dissertation entitled 
"Conformational Analysis of Polynucleotides at the Base-Base Level".
This work was done under the supervision of Prof. Wilma K. Olson at 
Rutgers University.  I believe since then another of her students 
has advanced the algorithm but I do not believe she is giving the 
program out yet.

>From [email-masked]
----------------------------

One other thing, I believe the trajectory analysis by 
G. Ravishanker is an adaptation of Lavery's curves.  You could, 
in theory, adopt any analysis program to analyze a trajectory by 
simply reading each frame and compiling the results.

>From [email-masked]
---------------------------------------

Write to:
		Richard Lavery
		Laboratoire de Biochimie Theorique URA 77 CNRS
		Institut de Biologie Physico-Chimique
		13 rue Pierre et Marie Curie
		Paris 75005 France

		Tel: 33 1 43 25 26 09
		Fax: 33 1 43 29 56 45

to obtain CURVES and JUMNA

>From [email-masked]
-----------------------------------

We have a general MD analysis package, with a total of 30 to 40 tools to
extract various properties of the system - solute properties, solvent
analysis, DNA specific, protein specific and protein-DNA complex specific
tools. One component of this is called the dials and windows. We have
modules to perform persistence analysis for bending analysis of DNA, other
forms of this called the bending dials, new ways of measuring the
groovewidths, extracting the "spine of hydration" in the grooves and doing
statistical analysis on them amongst other things. We have several other
utility modules (over 20) that perform very GROMOS specific tasks, such as
coordinate coversions. We are adding a new set of tools to do NMR property
calculations, such as the nOe buildup curves, T1, T2, order parameters,
and coupling constants using generalized Karplus equation.

We have also beefed up the graphics considerably so the current version
produces graphics through our general-purpose scientific graphing facility
called DEVINE Graph. The next distribution will include MD Toolchest and
DEVINE Graph (currently supports X11 OSF/Motif and Postscript) and we are
planning to get it out by Feb 1994. We had plans to get it out in Nov. but
we are behind. If you need more info, please let me know. Thanks.

>From [email-masked]
-----------------------------------

I also wish to mention that our program set can be used to analyse static
structures, either one by one or in a compare mode and we have applied our
DNA tools to analyse all the decamers and dodecamers in the NDB maintained
by Helen Berman.

>From [email-masked]
-----------------------------------

............... The code currently runs on SGI, IBM RS6000 and CRAY
Y/MP. With minor modifications, one should be able to port to other
machines. We will soon port it to run on a PC running NeXTStep. It is
written in Fortran 77 and C.

	The underlying program that produces the variables for dials and
windows is Lavery's CURVES. The graphics is done by dials and windows.
However, one can interface it to any program, say newhelix with some
effort. I am trying to contact Dickerson to get the current NEWHELIX, so
that we can put in the necessary modules (but require users to get
NEWHELIX from Dickerson).

	The MD Toolchest library is so organized and a template fortran
program is given in the distribution that tells you how you can write your
own application easily, by letting the MDTC library do all the work of
processing the coordinates etc.