dc.contributor.author	Bag, Sukantadev
dc.contributor.author	Prentice, Michael B.
dc.contributor.author	Liang, Mingzhi
dc.contributor.author	Warren, Martin J.
dc.contributor.author	Roy Choudhury, Kingshuk
dc.contributor.funder	Science Foundation Ireland
dc.contributor.funder	Health Research Board
dc.contributor.funder	National Institutes of Health
dc.date.accessioned	2017-06-21T11:01:25Z
dc.date.available	2017-06-21T11:01:25Z
dc.date.issued	2016-06-13
dc.description.abstract	Background: Cryo-electron tomography (cryo-ET) enables 3D imaging of macromolecular structures. Reconstructed cryo-ET images have a “missing wedge” of data loss due to limitations in rotation of the mounting stage. Most current approaches for structure determination improve cryo-ET resolution either by some form of sub-tomogram averaging or template matching, respectively precluding detection of shapes that vary across objects or are a priori unknown. Various macromolecular structures possess polyhedral structure. We propose a classification method for polyhedral shapes from incomplete individual cryo-ET reconstructions, based on topological features of an extracted polyhedral graph (PG). Results: We outline a pipeline for extracting PG from 3-D cryo-ET reconstructions. For classification, we construct a reference library of regular polyhedra. Using geometric simulation, we construct a non-parametric estimate of the distribution of possible incomplete PGs. In studies with simulated data, a Bayes classifier constructed using these distributions has an average test set misclassification error of?<?5 % with upto 30 % of the object missing, suggesting accurate polyhedral shape classification is possible from individual incomplete cryo-ET reconstructions. We also demonstrate how the method can be made robust to mis-specification of the PG using an SVM based classifier. The methodology is applied to cryo-ET reconstructions of 30 micro-compartments isolated from E. coli bacteria. Conclusions: The predicted shapes aren’t unique, but all belong to the non-symmetric Johnson solid family, illustrating the potential of this approach to study variation in polyhedral macromolecular structures.	en
dc.description.sponsorship	Science Foundation Ireland (Short Term Travel Fellowship 06/RFP/GEN053 STTF 08, Research Frontiers Program (grant 07/REF/MA7F543), SFI Math Initiative); Health Research Board (HRA_POR/2011/111); NIH (Duke CTSA UL1TR001117)	en
dc.description.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	234
dc.identifier.citation	Bag, S., Prentice, M. B., Liang, M., Warren, M. J. and Roy Choudhury, K. (2016) 'Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions', BMC Bioinformatics, 17, 234 (14pp). doi: 10.1186/s12859-016-1107-5	en
dc.identifier.doi	10.1186/s12859-016-1107-5
dc.identifier.endpage	14
dc.identifier.issn	1471-2105
dc.identifier.journaltitle	BMC Bioinformatics	en
dc.identifier.startpage	1
dc.identifier.uri	https://hdl.handle.net/10468/4127
dc.identifier.volume	17
dc.language.iso	en	en
dc.publisher	BioMed Central	en
dc.relation.uri	https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1107-5
dc.rights	© 2016, Bag et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.	en
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/	en
dc.subject	Polyhedron graph	en
dc.subject	Incomplete polyhedral	en
dc.subject	Classification from incomplete data	en
dc.subject	Cryo electron tomography	en
dc.subject	Bacterial microcompartment	en
dc.title	Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions	en
dc.type	Article (peer-reviewed)	en

Classification of polyhedral shapes from individual anisotropically resolved cryo-electron tomography reconstructions

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