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]<mailto:[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]> [mailto:[EMAIL
PROTECTED]<mailto:[EMAIL PROTECTED]>] On Behalf Of lijo skb
Sent: Friday, April 18, 2008 10:06 AM
To: [email protected]<mailto:[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]<mailto:[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]> [mailto:[EMAIL
PROTECTED]<mailto:[EMAIL PROTECTED]>] On Behalf Of Angel Herraez
Sent: Friday, April 18, 2008 9:28 AM
To: [email protected]<mailto:[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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