JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories.BACKGROUND
 We developed a Java based Essential Dynamics toolkit called JED to compare the ED from multiple protein trajectories.  JED implements Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) as options to construct covariance (Q) or correlation (R) matrices.  JED output results as text files that include transformed coordinates for aligned structures, several metrics that quantify protein mobility, PCA modes with their eigenvalues, and displacement vector (DV) projections onto the top principal modes.  JED offers a convenient toolkit that encourages best practices in applying multivariate statistics methods to perform comparative studies of essential dynamics over multiple proteins. 
JED