Cross-correlation analysis in multidomain proteins

From: James Starlight (
Date: Thu Mar 13 2014 - 05:32:22 CDT

Dear NAMD users!

I'm looking for useful software or VMD plugin for analysis of
cross-correlation within of multi-domain protein to study allostery and
signal transmission in it.

In practice I have 2 domains joined by long coiled-coiled linker where
first domain is ligand sensitive and the second domain has native fluoresce
element. I'd like to monitor transduction of conformational changes from
first to the second domain during ligand binding seen in 100 ns accelerated
molecular dynamics.

I've already tried to use NAMD network view plugin analysis based on the
cross-correlation computation from the covariance matrix but found only
significant correlation within each of domains separately. Does anybody
known some alternative solutions for such analysis?

Thanks for help,


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