[Biopython] Question on your Methods in Enzymology paper

[Peter Cock]

On Wed, Aug 17, 2011 at 10:44 PM, Brandon Breitling wrote:
>
> Hi Mr. Lunt,
>
> My name is Brandon Breitling and I'm a statistics
> graduate student in the United States.  I was
> wondering if you had the scripts or code available
> from your "Inference of Direct Residue Contacts
> in Two-Component Signaling" paper.  I'm trying
> to see if I can do the same for a eukaryotic
> protein pair that my lab studies.
>
> I have created the concatenated strings dataset
> for my protein as described in your paper and
> have attempted to make scripts for the MI steps
> but would really be benefited if I could get
> them for the all steps in the Direct Coupling
> analysis.  If you could also email me the
> accession number for your dataset so that I
> can verify that I have the scripts working,
> that would be most appreciated as well.
>
> Regards,
> Brandon Breitling

Hi Brandon,

It looks like you've mixed up your email addresses.

As it happens I did my PhD on TCS, and used
Biopython's Bio.PDB model to get crude distances
from a PDB complex (and also looked at MI). I'm
not sure if I've read this paper though...

Bryan Lunt, Hendrik Szurmant, Andrea Procaccini,
James A. Hoch, Terence Hwa and Martin Weigt
"Chapter Two -  Inference of Direct Residue Contacts
in Two-Component Signaling". Methods in Enzymology
Volume 471, 2010, Pages 17-41
http://dx.doi.org/10.1016/S0076-6879(10)71002-8

Peter