PhD Seminar • Bioinformatics — Protein Structure Elastic Network Model Normal Mode Analysis and the Rank 3 Positive Semidefinite Matrix Manifold

Xiao-Bo Li, PhD candidate
David R. Cheriton School of Computer Science

Elastic network models model a protein structure as a network of nodes, where neighbouring nodes are connected by springs. A Hookean spring potential energy is used to model nearby pairwise atomic interactions. This model allows the normal mode displacements of the protein to be calculated efficiently. Squaring the inter-atomic distance in the Hookean potential gives a new potential that is a function of the PSD Gram matrix. The PSD potential suggests the PSD Gram matrix is another object that can be used to model protein dynamics. Some mathematical consequences of this approach will be discussed.