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PLoS One. 2017 Aug 17;12(8):e0183057. doi: 10.1371/journal.pone.0183057. eCollection 2017.

Data-driven coarse graining of large biomolecular structures.

Author information

1
Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
2
Department of NMR based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
3
Felix Bernstein Institute for Mathematical Statistics in the Biosciences, Georg August University Göttingen, Goldschmidtstrasse 7, 37077 Göttingen, Germany.

Abstract

Advances in experimental and computational techniques allow us to study the structure and dynamics of large biomolecular assemblies at increasingly higher resolution. However, with increasing structural detail it can be challenging to unravel the mechanism underlying the function of molecular machines. One reason is that atomistic simulations become computationally prohibitive. Moreover it is difficult to rationalize the functional mechanism of systems composed of tens of thousands to millions of atoms by following each atom's movements. Coarse graining (CG) allows us to understand biological structures from a hierarchical perspective and to gradually zoom into the adequate level of structural detail. This article introduces a Bayesian approach for coarse graining biomolecular structures. We develop a probabilistic model that aims to represent the shape of an experimental structure as a cloud of bead particles. The particles interact via a pairwise potential whose parameters are estimated along with the bead positions and the CG mapping between atoms and beads. Our model can also be applied to density maps obtained by cryo-electron microscopy. We illustrate our approach on various test systems.

PMID:
28817608
PMCID:
PMC5560709
DOI:
10.1371/journal.pone.0183057
[Indexed for MEDLINE]
Free PMC Article

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