Figure 2

Analysis Features of MAVEN. A) Within MAVEN, we plot the anisotropic displacement tensors from PDB file 1T3R in red and computed from weighted ANM in blue. B) How strongly the directions of motion of eight parts of the protease structure are correlated with one another in the first mode of motion is summarized. C) We display three frames in a top-down view of the animation of mode 1 that was exported to PyMOL: the negative mode direction (left), the initial structure (center), and the positive mode deformation (right). Coloring and tube thickness is by B-factor. D) Visualization of the NMR ensemble described in PDB file 2KTD in PyMOL. Coloring is blue to red from the N to C-terminus. E) Principal Component Analysis of the ensemble is performed and the variance in each PC and the cumulative variance plotted. F) Computation of the cumulative overlap between a set of low frequency modes generated from the first member of the ensemble and the first 3 PCs, using equation 6. MAVEN always displays a heatmap, but only displays text for significant relationships (CO > 0.5).