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Figure 2 | BMC Bioinformatics

Figure 2

From: Integrating protein structural dynamics and evolutionary analysis with Bio3D

Figure 2

Results of ensemble PCA and NMA on E. coli DHFR. (A) Available PDB structures projected onto their first two principal components accounting for a total of 59% of the total variance. (B) Comparison of mode fluctuations calculated for open (black) and closed (red) conformations. The figure is generated by automated functions for plotting and the identification of areas of significant differences in residue fluctuations between groups of conformers (light blue boxes). The locations of major secondary structure elements are shown in the plot margins with β strands in gray and α helices in black. (C) Conformational ensemble obtained from interpolating along the first five modes of all collected E. coli structures. Domain analysis on the generated ensemble reveals the identification of two dynamic sub-domains colored red and blue, respectively. See Additional file 2 for full details and corresponding code for this analysis.

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