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
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-----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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