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Fig. 7 | BMC Bioinformatics

Fig. 7

From: JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit

Fig. 7

a For the entire TEM-1 protein, the scree plot for explicit all atom PCA is compared to HPCA using 1, 2, 3 eigenresidues to show that the captured variance approaches that of the exact variance. b Iterated RMSIP for HPCA is shown for 1, 2, and 3 eigenresidues compared to the eigenvectors found by explicit all atom PCA analysis. Using only a single eigenresidue per amino acid already reconstructs the explicit analysis up to 80% and including more degrees of freedom improves this to 95%

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