Research article Special Issues

Fast and accurate conversion of atomic models into electron density maps

  • Received: 01 February 2015 Accepted: 11 March 2015 Published: 17 March 2015
  • New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM) of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.

    Citation: O.S. Sorzano Carlos, Vargas Javier, Otón Joaquín, Abrishami Vahid, M. de la Rosa-Trevín José, del Riego Sandra, Fernández-Alderete Alejandro, Martínez-Rey Carlos, Marabini Roberto, M. Carazo José. Fast and accurate conversion of atomic models into electron density maps[J]. AIMS Biophysics, 2015, 2(1): 8-20. doi: 10.3934/biophy.2015.1.8

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  • New image processing methodologies and algorithms have greatly contributed to the signi cant progress in three-dimensional electron microscopy (3DEM) of biological complexes we have seen over the last decades. Naturally, the availability of accurate procedures for the objective testing of new algorithms is a crucial requirement for the further advancement of the eld. A good and accepted testing work ow involves the generation of realistic 3DEM-like maps of biological macromolecules from which some measure of ground truth can be derived, ideally because their 3D atomic structure is already known. In this work we propose a very accurate generation of maps using atomic form factors for electron scattering. We thoroughly review current approaches in the eld, quantitatively demonstrating the bene ts of the new methodology. Additionally, we study a concrete example of the use of this approach for hypothesis testing in 3D Electron Microscopy.
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    © 2015 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)
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