1. Exploring the Suitability of Coarse-Grained Techniques for the Representation of Protein Dynamics 
Agustí Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco 
Biophysical Journal 
Volume 95, Issue 5, Pages (September 2008)
DOI: /biophysj
Copyright © 2008 The Biophysical Society Terms and Conditions

2. Figure 1
Total variances (in Å2) computed for the set of proteins using MD (dark gray), BD (gray), and DMD (light gray).
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

3. Figure 2
Entropies (in cal/molK) associated with the samplings obtained using MD (dark gray), BD (gray), and DMD (light gray).
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

4. Figure 3
Harmonic force constants (kcal/mol Å2) associated with the deformation along eigenvectors derived from MD (blue), BD (red), and DMD (green) for representative proteins. The inset corresponds to values obtained for the first 10 eigenvectors.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

5. Figure 4
Dimensionality (top) and number (bottom) of essential modes required to explain 90% of the variance for the set of proteins using MD (dark gray), BD (gray), and DMD (light gray).
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

6. Figure 5
Rank distance between the DMD (light gray) or BD (gray) eigenvectors (x axis) and the MD eigenvectors showing the best overlap for representative proteins.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

7. Figure 6
Normalized spread (Eq. 21) of DMD (light gray) and BD (gray) eigenvectors in MD essential space.
Biophysical Journal  , DOI: ( /biophysj )
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8. Figure 7
Similarity index (γ; Eq. 19) between MD and coarse-grained important spaces in DMD (light gray) and BD (gray) simulations for the set of proteins. The important space is defined for each protein as (top) the minimum number of eigenvectors required to explain 90% of variance, and (bottom) the first 50 eigenvectors were selected for all proteins.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

9. Figure 8
Z-scores (Eq. 20) associated with similarity indices (Eq. 19 and Fig. 7) between MD and coarse-grained models with DMD (light gray) and BD (gray). The important space is defined for each protein as (top) the minimum number of eigenvectors required to explain 90% of variance and (bottom) the first 50 eigenvectors.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions

10. Figure 9
α-Carbons B-factors (in Å2) computed from MD (blue), DMD (green), and BD (red) simulations for representative proteins.
Biophysical Journal  , DOI: ( /biophysj )
Copyright © 2008 The Biophysical Society Terms and Conditions