Dimensionality reduction and correlation of biomolecular motions

Sakuraba, Shun

In this review, we explain dimensionality reduction techniques applied in the field of the biomolecular simulation. The methods based on the linear transformation are reviewed. We also investigate how these methods use correlation for reducing the dimension of biomolecules. Our review includes functional mode analysis, principal component analysis, full correlation analysis, quasi anharmonic analysis, and independent subspace analysis. We also discuss the physical interpretation and implications of the methods.