Joe,
Well, I think , I went wrong on putting the things across. Let me explain
the issue more simply. I have set of amino acid sequences in my hand and no
net work PPI information. This is my interest, if I load these sequence into
an application (say Jmol, may not be possible), it would display that
particular protein is related to Hub or Non hub. More simple- how I can say
one protein is hub or non- hub by using any computational method.
Lijo
On Fri, Apr 18, 2008 at 7:04 PM, Joe Ivanic [Contractor, Foreign National] <
[EMAIL PROTECTED]> wrote:
> In a protein-protein interaction (PPI) network, each protein is treated as
> a node. In this way there are a number of nodes ("atoms") and edges
> ("bonds") between them, and the PPI is now a simple network. So one can
> optimize a cheap energy functional for the molecule, in which the bonds have
> a harmonic type potential and non-bonded nodes have a weak repulsive force.
> Approximating the Hessian is tricky but I have a very interesting way. Did I
> forget to mention that PPI networks can have tens of thousands of proteins
> and interactions? This is why a viewing tool is useful. There are a few
> around, e.g., Cytoscape, but for real freedom, Jmol is ideal. However, you
> must be able to determine some sort of network geometry. This is the
> bottleneck.
>
> In this way, one can view any network with Jmol, by treating it as a big
> molecule. Using Jmol commands, various color schemes can be applied. I think
> my attachments have now just come through so you can see an example.
>
> Joe
>
>
> ---
>
> Dr. Joe Ivanic - Contractor, Foreign National
> Scientist
> Biotechnology HPC Software Applications Institute
> ATTN: MCMR-TT
> Building 363, Miller Drive
> Ft. Detrick, MD 21702-5012
>
> Voice: (301) 619 1976
> Fax: (301) 619 1983
>
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:
> [EMAIL PROTECTED] On Behalf Of Angel Herraez
> Sent: Friday, April 18, 2008 9:28 AM
> To: [email protected]
> Subject: Re: [Jmol-users] Hub and Non-Hub
>
> El 18 Apr 2008 a las 18:48, lijo skb escribió:
>
> > Joe and Angel,
> >
> > In my case, I have only amino acid sequences for each protein from the
> > lab.
>
> If you don't have 3D coordinates for the atoms (at least the alpha
> carbons), Jmol can do nothing for you.
>
>
>
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--
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Centre for Bioinformatics,
University of Kerala, India.
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