Joe,
Sorry, in fact I am in search of such option under any molecular
visualization tools. I understood the dilemma. I defer to the definition you
stated before on hub and non-hub. So let me ask, if I have coordinates
details from PDB for a protein sequence can I differentiate them into
hub/non hub.
Lijo
On Fri, Apr 18, 2008 at 7:45 PM, Joe Ivanic [Contractor, Foreign National] <
[EMAIL PROTECTED]> wrote:
> Lijo,
>
> Well, now I am confused. What are your definitions of "Hub" and "Non hub"
> ? and which appliations are you talking about in particular?
>
> You need a geometry file to read into Jmol. Jmol won't automatically
> generate a geometry from just a protein sequence. In fact, I'd like to know
> of any method that (accurately) can for any arbitrary protein, this is a
> topic of substantial research endeavours. E.g., protein folding.
>
> 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
>
>
> ------------------------------
> *From:* [EMAIL PROTECTED] [mailto:
> [EMAIL PROTECTED] *On Behalf Of *lijo skb
> *Sent:* Friday, April 18, 2008 10:06 AM
>
> *To:* [email protected]
> *Subject:* Re: [Jmol-users] Hub and Non-Hub
>
> 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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>
>
>
> --
> Manger Projects,
> SooryaKiran Bioinformatics,
> Centre for Bioinformatics,
> University of Kerala, India.
> +91 4714060948(off)
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University of Kerala, India.
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+91 9446515705(res)
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