Entropy estimates obtained for all systems.

<p>Alkane test systems butane to decane, dialanine, the 14-residue -turn, as well as free and complexed TATA box binding protein (TBP) cofactor. : absolute configurational entropy obtained by TI (in J/(mol K)); : direct density estimate without clustering; : sum of density estimates after subspace clustering; and : Mutual information expansion estimates of 2nd (MIE2) and 3rd order (MIE3); : size of largest cluster; : QH entropy estimate.</p

Principle of fill modes.

<p>a) Two arbitrarily correlated modes and marginally distributed on the axes. Correlation is clearly visible from the -distributed . The joint distribution is more sparsely sampled than both marginal distributions. b) The -distributed is decorrelated and has exactly as many sample points as the joint distribution in a), allowing precise computation of .</p

Entropy estimates for a set of small test systems.

<p>Five selected alkane systems, dialanine (left), and the C-terminal turn of Protein G (right, please note that here the units are kJ/(mol K)). Thermodynamic integration (TI), density estimates over the whole configurational space (dir), full correlation analyis with subsequent clustering and kernel density estimation (FCA), quasi-harmonic (QH) and mutual information expansion estimates of 2nd (MIE2) and 3rd (MIE3) order were obtained as described in the text.</p

Entropy estimates for the TATA box binding protein (TBP) inhibitor in complex (left) and free (right).

<p>The following techniques are used: quasi-harmonic approximation (QH); FCA with subsequent density estimation using a high clustering threshold (hi thresh) or, respectively, a low threshold (lo thresh); mutual information expansion of order 2 (MIE2) or, respectively, of order 3 (MIE3). The displayed entropy estimates are averages over five independent simulations of 100 ns each, the error bars indicate standard deviations of the mean.</p

These 34 dynamics observables to have been used to characterize the dynasome.

<p>These 34 dynamics observables to have been used to characterize the dynasome.</p

These 24 structure observablesto have been used to characterize the protein structure space.

<p>These 24 structure observablesto have been used to characterize the protein structure space.</p

Projection of the dynasome onto descriptors 1 and 2.

<p>Each point represents one protein. <b>a)</b> Protein dynamics as described by dynasome descriptors 1 and 2. The axes labels indicate which dynamics properties are mainly described by the respective descriptor. The inset focuses on the lower left region. <b>b)</b> same projection as in <b>a)</b>, colored according to SCOP structure classes (see legend). Ellipses indicate the distributions of structure classes; Large thin ellipses denote standard deviations of the distributions, small thick ellipses the standard deviations of their mean.</p

Recovery of structural classes from dynamics.

<p>Distribution of three <b>a)</b> and all five <b>b)</b> SCOP classes (colors) onto partitionings of the dynasome (1…5) obtained from k-means clustering. Bar heights denote the fraction of proteins of each structure class found in each partition.</p

Eigenvalue spectrum of the collective dynamics descriptors

<p>Eigenvalues are given as fractions of the sum of all eigenvalues. The inset shows the cumulative distribution.</p

Distribution of proteins in <i>structure</i> space.

<p>Each point represents one protein. <b>a)</b> Protein structures as described by eigenvectors 1 and 2. In plot <b>a)</b> the same proteins as in Fig. 3 are labelled. <b>b)</b> same projection as in <b>a)</b>, but colored according to SCOP structure classes (see legend). Distributions of SCOP classes are described by their standard deviations (thin large ellipses) as well as the standard deviation of their respective means (thick small ellipses).</p