[Biodevelopers] binding energy calculation

[Joe Landman]

I am not sure if you want to consider commercial codes, but DNA Software
in Ann Arbor MI has something like this in OMP.

http://dnasoftware.com/

On Mon, 2003-10-06 at 16:53, Patrick McConnell wrote:
> 
> 
> 
> Good pointer, but I need some a little more sophisticated than Tm.  Tm is
> probably sufficient for short probes, but I am looking for something more
> general that I can apply for gene-to-gene interactions.   This would
> include things like base stacking, take into account hairpin loops in the
> gene match, etc.
> 
> -Patrick
> 
> 
> 
> 
> 
> Titus Brown <titus at caltech.edu>@bioinformatics.org on 10/06/2003 04:44:08
> PM
> 
> Please respond to biodevelopers at bioinformatics.org
> 
> Sent by:    biodevelopers-admin at bioinformatics.org
> 
> 
> To:    biodevelopers at bioinformatics.org
> cc:
> 
> Subject:    Re: [Biodevelopers] binding energy calculation
> 
> -> Does anyone know of a tool to calculate the binding affinity between
> -> between a short mRNA probe and a gene?  I am familiar with mfold and the
> -> vienna rna package, which perform similar calculations (correct me if I
> am
> -> wrong here), but they calculate energies for self-binding.
> 
> Google for 'melting temperature' or 'annealing' instead.  The first hit
> is this:
> 
>              http://www.retrogen.com/index/melting_template.htm
> 
> cheers,
> --titus
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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615