Abstract
“Elastic network interpolation (ENI)” generates a series of transitional conformations between two protein conformations by interpolating inter-atomic distances. A group of atoms that maintain their inter-atomic distances while moving concurrently in a protein is known as a rigid cluster; “rigid cluster ENI” is the interpolation of the rotations and translations of rigid clusters. Rank 3 positive semidefinite (PSD) matrix manifolds have faces that are defined by these rigid clusters. This facial structure strongly suggests that these matrix manifolds are a natural choice for modelling rigid cluster transitions. In this paper, we show that rigid cluster ENI can be formulated as a facially reduced rank 3 PSD matrix manifold optimization problem.