• ## Outreach

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Tue Oct 07 2014 - 11:12:52 CDT

Hi Mason,

In the original implementation of the Dynamical Network Analysis, the path
lengths are related to the correlation of motion between residues involved
in the edges along the path. As a result, the absolute values of the
distance in suboptimal pathways can be related to the drop off in
correlation of residues along the suboptimal pathway (when compared to the
optimal one), i.e., the distance is 4.5 compared to 3 - the drop off of
correlation of edges along the pathway is 10^1.5. When you use relative
values, you lose this power. I dont think there is anything wrong with it
otherwise.

Anurag

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

On Tue, Sep 30, 2014 at 8:39 PM, mason H <tailermason_at_gmail.com> wrote:

> Hello,
> I have a question regarding "Pathway analysis" in the "Dynamical
> Network Analysis" tutorial.
> After running the 'subopt' routine to generate a list of optimal and
> suboptimal pathways, I opened the output file ("subopt.out.out") and
> noticed that the paths are listed and it shows the path length in
> parenthesis. Here is an example (with arbitrary node numbers and path
> lengths):
>
> Path 0 = 888, 1, 3, 5, 999, (300)
> Path 1 = 888, 2, 4, 6, 999, (450)
> Path 2 = 888, 3, 6, 9, 999, (600)
>
> I have a question regarding the path length values.
>
> Instead of reporting path length values of:
> Path 0 length = 300
> Path 1 length = 450
> Path 2 length = 600
>
> Can I instead list only the relative values of:
> Path 0 length = 1.0
> Path 1 length = 1.5
> Path 2 length = 2.0
>
> While this would seem logical and straightforward, I just want to make
> sure that listing the values as a ratio instead of their listed path length
> is ok
>
> Thank you.
>