Joe, thanks for the kind information.
Lijo Anto M.A
Manger Projects,
SooryaKiran Bioinformatics,
Centre for Bioinformatics,
University of Kerala, India.
+91 4714060948(off)
+91 9446515705(res)
On Fri, Apr 18, 2008 at 8:10 PM, Joe Ivanic [Contractor, Foreign National] <
[EMAIL PROTECTED]> wrote:
> Lijo,
>
> If you are referring to the definition of "hub" as it applies to
> protein-protein interaction (PPI) networks, then you need to have "a" PPI
> network in order to see how many interactions a particular protein has. At
> the minimum you need to know how many interactions a protein has (or its
> degree), not necessarily its interaction partners. As far as I know, there
> is not a 100% way to tell from the sequence alone whether a protein will
> have many interaction partners. This is also a topic of much research.
>
> There are a number of sites that curate PPI networks. The web site below
> contains links to many of them:
>
> http://www.nature.com/cr/journal/v18/n2/fig_tab/cr200816t1.html
>
> 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 10:31 AM
>
> *To:* [email protected]
> *Subject:* Re: [Jmol-users] Hub and Non-Hub
>
> 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)
> > +91 9446515705(res)
> >
> >
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>
> --
> Manger Projects,
> SooryaKiran Bioinformatics,
> Centre for Bioinformatics,
> University of Kerala, India.
> +91 4714060948(off)
> +91 9446515705(res)
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference
> Don't miss this year's exciting event. There's still time to save $100.
> Use priority code J8TL2D2.
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--
Manger Projects,
SooryaKiran Bioinformatics,
Centre for Bioinformatics,
University of Kerala, India.
+91 4714060948(off)
+91 9446515705(res)
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