<p>Labels of 1 and 2 in the landscapes represent the initial (left) and the final (right) structures at 0 ns and 40 ns, respectively. Color codes: negatively charged residues (<i>red</i>), positively charged residues (<i>blue</i>), hydrophilic residues (<i>green</i>), and hydrophobic residues (<i>white</i>). C<sub>β</sub> atoms of Met35 are shown by VDW spheres to guide eyes. All cartoon structures are rendered by VMD <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0020575#pone.0020575-Humphrey1" target="_blank">[62]</a>.</p
The binding energy (Kcal mol-1) is plotted versus DSite and DConf for each of the ssDBP–ssDNA (top, ...
<p>Top panel: contact maps in water, against reference PDB structure (in black) for the IRF-3 and AC...
<p>(A) Cartoon representation of the NMR structure of the α-helical domain of M2-1<sub>58–177</sub> ...
Sketch-map projected RMD data. Black circular shapes: rim of combined landscape of all linkage types...
<p>Panels A and B show the RMSD per residue of the WT MPP and ΔGRL MPP structures, respectively. The...
<p>The maps indicate regions of negative potential in red, positive potential in blue, and neutral p...
<p>A) Plot of number of residue correspondences vs. RMSD in each structure (d1gt8a4 is in green, d1m...
<p><b> monomers and dimers with representative conformations. </b><i>The reaction coordinates are th...
<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the...
<p>a) Cartoon drawing of the lowest energy conformer of CTD. The two monomers are indicated by two d...
<p>A) Representative structures of the conformational sub-states of the C-terminal stretch (marked i...
<p>The red point indicates the energy minimised crystal structure loop and the blue point indicates ...
<p>The unit of the free energy is kcal/mol. Multiple representative structures are given for the fir...
<p>Each point represents a unique conformation. The color indicates energy with darker colors repres...
<p>A schematic energy landscape and a schematic free energy landscape are shown in (A) and (B), resp...
The binding energy (Kcal mol-1) is plotted versus DSite and DConf for each of the ssDBP–ssDNA (top, ...
<p>Top panel: contact maps in water, against reference PDB structure (in black) for the IRF-3 and AC...
<p>(A) Cartoon representation of the NMR structure of the α-helical domain of M2-1<sub>58–177</sub> ...
Sketch-map projected RMD data. Black circular shapes: rim of combined landscape of all linkage types...
<p>Panels A and B show the RMSD per residue of the WT MPP and ΔGRL MPP structures, respectively. The...
<p>The maps indicate regions of negative potential in red, positive potential in blue, and neutral p...
<p>A) Plot of number of residue correspondences vs. RMSD in each structure (d1gt8a4 is in green, d1m...
<p><b> monomers and dimers with representative conformations. </b><i>The reaction coordinates are th...
<p>(A) Free energy landscape of metadynamics simulation. The brown dotted outline corresponds to the...
<p>a) Cartoon drawing of the lowest energy conformer of CTD. The two monomers are indicated by two d...
<p>A) Representative structures of the conformational sub-states of the C-terminal stretch (marked i...
<p>The red point indicates the energy minimised crystal structure loop and the blue point indicates ...
<p>The unit of the free energy is kcal/mol. Multiple representative structures are given for the fir...
<p>Each point represents a unique conformation. The color indicates energy with darker colors repres...
<p>A schematic energy landscape and a schematic free energy landscape are shown in (A) and (B), resp...
The binding energy (Kcal mol-1) is plotted versus DSite and DConf for each of the ssDBP–ssDNA (top, ...
<p>Top panel: contact maps in water, against reference PDB structure (in black) for the IRF-3 and AC...
<p>(A) Cartoon representation of the NMR structure of the α-helical domain of M2-1<sub>58–177</sub> ...