This thesis investigates dimensionality reduction for analyzing the dynamics of

protein simulations, particularly disordered proteins which do not fold into a xed

shape but are thought to perform their functions through their movements. Rather

than analyze the movement of the proteins in 3D space, we use dimensionality

reduction to project the molecular structure of the proteins into a target space in

which each structure is represented as a point. All that is needed to do this are

the pairwise distances between the protein structures. We can then visualize the

projected structures in three dimensions to get a general idea of the dynamics of

the protein. We can also measure how well the projection preserves the pairwise

distances between structures for a particular target dimension to get an idea of

the dimension of the dynamics of the protein in the original space.