Analyzing Protein Dynamics Using Dimensionality Reduction
- Author(s): Eryol, Atahan
- Advisor(s): Newsam, Shawn
- et al.
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.