A Method for Correlations Analysis of Coordinates: Applications for Molecular Conformations.

We describe a new method to analyze multiple correlations between subsets of coordinates that represent a sample. The correlation is established only between specific regions of interest at the coordinates. First, the region(s) of interest are selected at each molecular coordinate. Next, a correlation matrix is constructed for the selected regions. The matrix is subject to further analysis, illuminating the multidimensional structural characteristics that exist in the conformational space. The method's abilities are demonstrated in several examples:  it is used to analyze the conformational space of complex molecules, it is successfully applied to compare related conformational spaces, and it is used to analyze a diverse set of protein folding trajectories.