Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control
Joint Authors
Jonić, Slavica
Sorzano, Carlos Oscar S.
Source
Issue
Vol. 2016, Issue 2016 (31 Dec. 2016), pp.1-11, 11 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2016-12-21
Country of Publication
Egypt
No. of Pages
11
Main Subjects
Abstract EN
Three-dimensional Gaussian functions have been shown useful in representing electron microscopy (EM) density maps for studying macromolecular structure and dynamics.
Methods that require setting a desired number of Gaussian functions or a maximum number of iterations may result in suboptimal representations of the structure.
An alternative is to set a desired error of approximation of the given EM map and then optimize the number of Gaussian functions to achieve this approximation error.
In this article, we review different applications of such an approach that uses spherical Gaussian functions of fixed standard deviation, referred to as pseudoatoms.
Some of these applications use EM-map normal mode analysis (NMA) with elastic network model (ENM) (applications such as predicting conformational changes of macromolecular complexes or exploring actual conformational changes by normal-mode-based analysis of experimental data) while some other do not use NMA (denoising of EM density maps).
In applications based on NMA and ENM, the advantage of using pseudoatoms in EM-map coarse-grain models is that the ENM springs are easily assigned among neighboring grains thanks to their spherical shape and uniformed size.
EM-map denoising based on the map coarse-graining was so far only shown using pseudoatoms as grains.
American Psychological Association (APA)
Jonić, Slavica& Sorzano, Carlos Oscar S.. 2016. Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control. BioMed Research International،Vol. 2016, no. 2016, pp.1-11.
https://search.emarefa.net/detail/BIM-1098658
Modern Language Association (MLA)
Jonić, Slavica& Sorzano, Carlos Oscar S.. Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control. BioMed Research International No. 2016 (2016), pp.1-11.
https://search.emarefa.net/detail/BIM-1098658
American Medical Association (AMA)
Jonić, Slavica& Sorzano, Carlos Oscar S.. Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control. BioMed Research International. 2016. Vol. 2016, no. 2016, pp.1-11.
https://search.emarefa.net/detail/BIM-1098658
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1098658