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Recent approaches to the study of biological molecules employ manifold learning to single-particle cryo-EM datasets to map the continuum of states of a molecule into a low-dimensional space spanned by eigenvectors, or "conformational coordinates". This is done separately for each projection direction (PD) on an angular grid. One important step in deriving a consolidated map of occupancies, from which the free energy landscape of the molecule can be derived, is to propagate the conformational coordinates from a given choice of "anchor PD" across the entire angular space. Even when one eigenvector dominates, its sign might invert from one PD to the next. The propagation of the second eigenvector is particularly challenging when eigenvalues of the second and third eigenvector are closely matched, leading to occasional inversions in their ranking as we move across the angular grid. In the absence of a computational approach, this propagation across the angular space has been done thus far "by hand" using visual clues, thus greatly limiting the general use of the technique. In this work we have developed a method that is able to solve the propagation problem computationally, by using optical flow and a probabilistic graphical model. We demonstrate its utility by selected examples.
This article was published in the following journal.
Name: Journal of chemical information and modeling
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A statistically significant excess of cases of a disease, occurring within a limited space-time continuum.
A distribution function used to describe the occurrence of rare events or to describe the sampling distribution of isolated counts in a continuum of time or space.
Rhythmic, intermittent propagation of a fluid through a BLOOD VESSEL or piping system, in contrast to constant, smooth propagation, which produces laminar flow.
Methods used for studying the interactions of antibodies with specific regions of protein antigens. Important applications of epitope mapping are found within the area of immunochemistry.
Protein domains that are enriched in PROLINE. The cyclical nature of proline causes the peptide bonds it forms to have a limited degree of conformational mobility. Therefore the presence of multiple prolines in close proximity to each other can convey a distinct conformational arrangement to a peptide chain.
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