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| - Can Principal Components Yield a Dimension Reduced Description of Protein Dynamics onLong Time Scales?
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| - The suitability of principal component analysis (PCA) to yield slow collective coordinates for use within adimension reduced description of conformational motions in proteins is evaluated. Two proteins are considered,T4 lysozyme and crambin. We present a quantitative evaluation of the convergence of conformationalcoordinates obtained with principal component analysis. Detailed analyses of (>200 ns) molecular dynamicstrajectories and crystallographic data suggests that simulations of a few nanoseconds should generally providea stable and statistically reliable definition of the essential and near constraints subspaces. Moreover, asystematic assessment of the density of states of the dynamics of all principal components showed that foran optimal separation of time scales it is crucial to include also side chain atoms in the PCA.
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