Xiao-Bo Li, PhD candidate
David R. Cheriton School of Computer Science
A protein structure's elastic network model (ENM) assumes neighboring atoms are connected by fictitious springs. Such a model has been used to generate transitional conformations between a given beginning and an ending conformation. One modelling approach, called the interpolated ENM (iENM), produces intermediate structures that model local change at an active site before global change. The ability of the model to distinguish local versus global structural changes supports the importance of local motions at an active site driving larger conformational changes.
In this seminar, we show the iENM model can be formulated as a rank 3 positive semidefinite (PSD) matrix manifold optimization problem. The use of the rank 3 PSD matrix manifold to model ENMs suggests ENMs can arise from using the rank 3 PSD matrix manifold as the Riemannian manifold for formulating the equations of motion, providing these models with more mathematical formalism.
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