Fwd: [External] Boost value in aMD simulation

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Thu Aug 21 2014 - 06:05:05 CDT

On 19 August 2014 21:45, James Starlight <jmsstarlight_at_gmail.com> wrote:

> Thanks for suggestions!
> Regarding simulation with the ligand: does the idea to perform clustering
> of the receptor's regions (loop) being interacting with different ligands
> seems good (e.g to compare results of apo-holo simulation to detect some
> shared clusters between bpoth systems)?
There are many things you can do. None can tell if something 's worth doing
or not but you. Notwithstanding, I wouldn't look for common clusters but I
would compare the predominant cluster representatives in the apo and holo
simulation to identify induced fit conformational changes in the ligand
binding region.

> Regarding cut-off: when I reduced it to 1-2 A I still obtain 6-7 clusters
> but most of the conformers were as the outliers (not in any of these
> clusters).
Vague statement. Cannot make conclusions without cluster numbers and

> Regarding dendrograms: for me better to find some python package for such
> task :-) I'll try to check for it! Might the g_cluster be also usefull
> within my taks besides of obtaining representative structures from each
> clusters?
This might help:


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