molecular dynamics
In molecular dynamics simulations, one if often looking for a stable configuration of a protein, since these are the ones that are most likely to be found in nature. In order to find these low-energy confirmations, one often looks at the singular value decomposition, since the left singular vectors of a trajectory (the columns of U) give us the major modes of motion that best describe the flexibility of the protein.
HIV1 Protease
For many molecules, there is an inherent form of symmetry within the molecule. An example of such a molecule is HIV1 Protease, which is essential in the replication of the HIV viron. For these symmetric proteins, if one could find a symmetry preserving singular value decomposition (SPSVD), then we would have major modes that best describe the flexible motions of the protein.
Comparison of SVD in red and SPSVD in blue.
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