This thesis investigates dimensionality reduction for analyzing the dynamics ofprotein simulations, particularly disordered proteins which do not fold into a xedshape but are thought to perform their functions through their movements. Ratherthan analyze the movement of the proteins in 3D space, we use dimensionalityreduction to project the molecular structure of the proteins into a target space inwhich each structure is represented as a point. All that is needed to do this arethe pairwise distances between the protein structures. We can then visualize theprojected structures in three dimensions to get a general idea of the dynamics ofthe protein. We can also measure how well the projection preserves the pairwisedistances between structures for a particular target dimension to get an idea ofthe dimension of the dynamics of the protein in the original space
