Re: the difference of PCA and EDA

From: Fotis Baltoumas (
Date: Wed Dec 10 2014 - 05:36:43 CST


There isn't much of a difference, actually. An Essential Dynamics Analysis
is, essentially (pun intended), PCA directed at seperating the
configurational space into two subspaces, a physically constrained
subspace describing local fluctuation and an “essential” subspace with a
few degrees of freedom in which anharmonic motion occurs that comprises
most of the positional fluctuations. Since the latter are considered to
be "essential" for protein behavior and function, this PCA is termed
"EDA". Whether you perform EDA on an MD trajectory or PCA on an NMR
ensemble, basically you're doing the same kind of calculations.

You can find more on the subject by reading Berendsen's original EDA paper:

And the following book chapter on Normal Mode Analysis, PCA and Essential
Dynamics can also be useful:

Hope I helped,
Fotis Baltoumas

> Dear all:
> We usually need to analyze the intrinsic collective motions from a
> trajectory.
> Does anybody know the difference between Principal Component Analysis
> and Essential Dynamic Analysis for a trajectory?
> Principal component analysis (PCA) is a statistical procedure that
> uses an orthogonal transformation to convert a set of observations of
> possibly correlated variables
> into a set of values of linearly uncorrelated variables called principal
> components.
> What about EDA?
> Thanks
> Xiaoying
> --
> Xiaoying Lv
> Department of Bioinfomatics
> Room C321, Medical Building
> Tsinghua University
> Beijing,China 100084
> Tel��010-62794737

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