2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
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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.
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