[Biopython] Biopython Digest, Vol 104, Issue 10

[Bryan Lunt]

Oh!,
Yeah, we used BioPython extensively, but I thought I sent Brandon the
code already...
We have a decent module for getting distances from Bio.PDB, though
unfortunately it uses far far too much disk space (it outputs a large
text file with every residue compared to every other reside, allowing
AWK or some other tool to filter the file.)
And a large set of tools for creating putative pairings, mainly for
TCS, but of course generalized to pair any set of protein domains...

-Bryan

On Thu, Aug 18, 2011 at 9:00 AM,  <biopython-request at lists.open-bio.org> wrote:
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> Today's Topics:
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>   1. Question on your Methods in Enzymology paper (Brandon Breitling)
>   2. Re: Question on your Methods in Enzymology paper (Peter Cock)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 17 Aug 2011 21:44:21 +0000 (UTC)
> From: Brandon Breitling <brandonjbreitling at gmail.com>
> Subject: [Biopython] Question on your Methods in Enzymology paper
> To: biopython at biopython.org
> Message-ID: <loom.20110817T233009-686 at post.gmane.org>
> Content-Type: text/plain; charset=us-ascii
>
>
> Hi Mr. Lunt,
>
> My name is Brandon Breitling and I'm a statistics
> graduate student in the United States.  I was
> wondering if you hadthe 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 17 Aug 2011 23:21:44 +0100
> From: Peter Cock <p.j.a.cock at googlemail.com>
> Subject: Re: [Biopython] Question on your Methods in Enzymology paper
> To: Brandon Breitling <brandonjbreitling at gmail.com>
> Cc: biopython at biopython.org
> Message-ID:
>        <CAKVJ-_5jp_2X-zqFDOnL68TpeQBB5BJWMHQ5nH9Fi3fsep_daQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
>
>
>
> ------------------------------
>
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> End of Biopython Digest, Vol 104, Issue 10
> ******************************************
>