2016Jonic Pseudoatoms

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Jonić, S. & Sorzano, C. O. S. Coarse-graining of volumes for modeling of structure and dynamics in electron microscopy: algorithm to automatically control accuracy of approximation IEEE J. Selected Topics in Signal Processing, 2016, 10, 161-173


Coarse-graining (or granularization) of structures from transmission electron microscopy (EM volumes) has been shown to be useful for a variety of structural analysis applications. Several methods perform coarse-graining of EM volumes using hard spheres or 3D Gaussian functions but they do not allow controlling automatically the volume approximation accuracy. To tackle this problem, we recently developed such a method. It is currently used by 3DEM Loupe web server and HEMNMA software to study macromolecular dynamics based on coarse-grained representations of EM volumes. In this paper, we give a detailed description of the implemented algorithm and fully analyze its performance, which was out of scope of our previous papers. The performance is analyzed in a controlled environment, in the context of studying structure and dynamics of macromolecular complexes. We show that this technique allows computing structures that are similar to atomic structures, by analyzing intermediate-resolution volumes. Additionally, we show that it allows sharpening of intermediate-resolution volumes. The full algorithm description allows its implementation in any other software package.




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