Publication: Procrustean rotation in concert with principal component analysis of molecular dynamics trajectories: Quantifying global and local differences between conformational samples

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Title	Procrustean rotation in concert with principal component analysis of molecular dynamics trajectories: Quantifying global and local differences between conformational samples
Authors/Editors*	D.G. Oblinsky, B.M.B. VanSchouwen, H.L. Gordon, S.M. Rothstein
Where published*	Journal of Chemical Physics
How published*	Journal
Year*	2009
Volume	131
Number
Pages	225102(1-8)
Publisher	American Institute of Physics
Keywords	molecular dynamics, principal component analysis, bootstrap resampling, Procrustean rotation
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Abstract	Given the principal component analysis PCA of a molecular dynamics MD conformational trajectory for a model protein, we perform orthogonal Procrustean rotation to âbest fitâ the PCA squared-loading matrix to that of a target matrix computed for a related but different molecular system. The sum of squared deviations of the elements of the rotated matrix from those of the target, known as the error of fit EOF, provides a quantitative measure of the dissimilarity between the two conformational samples. To estimate precision of the EOF, we perform bootstrap resampling of the molecular conformations within the trajectories, generating a distribution of EOF values for the system and target. The average EOF per variable is determined and visualized to ascertain where, locally, system and target sample properties differ. We illustrate this approach by analyzing MD trajectories for the wild-type and four selected mutants of the 1 domain of protein G.