Journal Article

A framework to refine particle clusters produced by EMAN

Liya Fan, Fa Zhang, Gongming Wang and Zhiyong Liu

in Bioinformatics

Volume 25, issue 12, pages i276-i280
Published in print June 2009 | ISSN: 1367-4803
Published online May 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp219

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Motivation: EMAN is one of the most popular software packages for single particle reconstruction. But the particle clusters produced during its model refining stage are of low qualities. We attempt to refine the particle clusters by more accurately determining orientations of particles, and thereby achieving higher resolutions of consequent 3D structures.

Results: A particle reclustering framework (PRF) is introduced, which consists of three components. Each of them is responsible for one of the basic tasks of PRF: normalization, threshold determination and reclustering. Our implementation is also described and proved to meet the constraints proposed by PRF. Experiments revealed that our implementation improved resolutions of consequent structures for most cases, but only a little extra execution time was incurred. Therefore, it is practical to incorporate PRF in EMAN to improve qualities of generated 3D structures.

Availability and Implementation: Implementation of our algorithm is available upon request from the authors.

Contact: fanliya@ict.ac.cn; zf@ncic.ac.cn

Journal Article.  3259 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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