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  Fast and accurate reference-free alignment of subtomograms

Chen, Y., Pfeffer, S., Hrabe, T., Schuller, J. M., & Förster, F. (2013). Fast and accurate reference-free alignment of subtomograms. JOURNAL OF STRUCTURAL BIOLOGY, 182(3), 235-245. doi:10.1016/j.jsb.2013.03.002.

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 Creators:
Chen, Yuxiang1, Author              
Pfeffer, Stefan1, Author              
Hrabe, Thomas1, Author              
Schuller, Jan Michael2, Author              
Förster, Friedrich2, Author              
Affiliations:
1Baumeister, Wolfgang / Molecular Structural Biology, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565142              
2Förster, Friedrich / Modeling of Protein Complexes, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565148              

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Free keywords: CRYOELECTRON TOMOGRAPHY; ELECTRON TOMOGRAPHY; IN-SITU; 3-DIMENSIONAL STRUCTURE; VISUAL PROTEOMICS; SINGLE PARTICLES; CLASSIFICATION; MICROSCOPY; EM; MACROMOLECULESCryo-electron tomography; Subtomogram averaging; Spherical harmonics;
 Abstract: In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20 angstrom and 16 angstrom, respectively. The software is ready-to-use and made public to the community. (c) 2013 Elsevier Inc. All rights reserved.

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Language(s): eng - English
 Dates: 2013-06
 Publication Status: Published in print
 Pages: 11
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: ISI: 000320012500005
DOI: 10.1016/j.jsb.2013.03.002
 Degree: -

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Title: JOURNAL OF STRUCTURAL BIOLOGY
Source Genre: Journal
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Publ. Info: 525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA : ACADEMIC PRESS INC ELSEVIER SCIENCE
Pages: - Volume / Issue: 182 (3) Sequence Number: - Start / End Page: 235 - 245 Identifier: ISSN: 1047-8477