VMD-L Mailing List

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Mon Sep 01 2014 - 14:05:21 CDT

Ben,

As you know, the idea of Dynamical Network Analysis is to look at the
mechanism by which non-covalent contacts lead to communication between
distant parts of a protein. When we tried to use backbone contacts for
calculating optimal and suboptimal paths, the bonding interactions
dominated and led to very trivial changes in suboptimal paths - this is
partly because neighboring residues in an MD simulation of a protein tend
 to be very highly correlated in motion making the distance between these
nodes in the network negligible. In order to separate the signal from the
bonded interactions from the non-bonded interactions, we chose to not place
edges between neighboring residues in the protein. However, if u have large
timescale simulations or large conformational changes in the protein during
the timescale of your simulations, it might be worth comparing the results
with and without the restrictions.

Cheers,
Anurag
ᐧ

Genius is nothing more or less than doing well what anybody can do badly. -
Amelia Barr

On Mon, Sep 1, 2014 at 2:27 PM, mason H <tailermason_at_gmail.com> wrote:

> I am performing Dynamical Network Analysis on my protein. I am using the
> built-in 'networkSetup' VMD script. One residue is one 'node'.
> I have a question on >RESTRICTIONS that get listed in the networkSetup
> input file.
>
> In most procedures I have seen so, they use the 'NotNeighboringResidue'
> and 'NotSameResidue' restriction.
>
> Except for 'NotSameResidue', Is it ever ok to have NO restrictions when
> looking at networks within a protien? Why can I not allow for edges
> between consecutively numbered residues?
>
> (FYI: In my case, my protein is 400 residues and, for the record, I am
> looking at optimal and suboptimal paths between two different regions of a
> protein about 25 Angstroms apart. I am wondering why I would prevent a
> path from traversing along consecutively numbered residues)
>
>
> Thank you,
> Ben
>