REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers
Abstract Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computational algorithms (“pickers”) identify different particle sets, complicating the selection of the best-su...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-10-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-024-07045-0 |
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| author | Christopher J. F. Cameron Sebastian J. H. Seager Fred J. Sigworth Hemant D. Tagare Mark B. Gerstein |
| author_facet | Christopher J. F. Cameron Sebastian J. H. Seager Fred J. Sigworth Hemant D. Tagare Mark B. Gerstein |
| author_sort | Christopher J. F. Cameron |
| collection | DOAJ |
| description | Abstract Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computational algorithms (“pickers”) identify different particle sets, complicating the selection of the best-suited picker for a protein of interest. Here, we present REliable PIcking by Consensus (REPIC), a computational approach to identifying particles common to the output of multiple pickers. We frame consensus particle picking as a graph problem, which REPIC solves using integer linear programming. REPIC picks high-quality particles even when the best picker is not known a priori or a protein is difficult-to-pick (e.g., NOMPC ion channel). Reconstructions using consensus particles without particle filtering achieve resolutions comparable to those from particles picked by experts. Our results show that REPIC requires minimal (often no) manual intervention, and considerably reduces the burden on cryo-EM users for picker selection and particle picking. Availability: https://github.com/ccameron/REPIC . |
| format | Article |
| id | doaj-art-fe00cb92b6fb48f3bf722ecef3f5348e |
| institution | OA Journals |
| issn | 2399-3642 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Nature Portfolio |
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| series | Communications Biology |
| spelling | doaj-art-fe00cb92b6fb48f3bf722ecef3f5348e2025-08-20T02:18:35ZengNature PortfolioCommunications Biology2399-36422024-10-017111210.1038/s42003-024-07045-0REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickersChristopher J. F. Cameron0Sebastian J. H. Seager1Fred J. Sigworth2Hemant D. Tagare3Mark B. Gerstein4Department of Molecular Biophysics and Biochemistry, Yale UniversityDepartment of Molecular Biophysics and Biochemistry, Yale UniversityDepartment of Molecular Biophysics and Biochemistry, Yale UniversityDepartment of Radiology and Biomedical Imaging, Yale UniversityDepartment of Molecular Biophysics and Biochemistry, Yale UniversityAbstract Cryo-EM particle identification from micrographs (“picking”) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. State-of-the-art computational algorithms (“pickers”) identify different particle sets, complicating the selection of the best-suited picker for a protein of interest. Here, we present REliable PIcking by Consensus (REPIC), a computational approach to identifying particles common to the output of multiple pickers. We frame consensus particle picking as a graph problem, which REPIC solves using integer linear programming. REPIC picks high-quality particles even when the best picker is not known a priori or a protein is difficult-to-pick (e.g., NOMPC ion channel). Reconstructions using consensus particles without particle filtering achieve resolutions comparable to those from particles picked by experts. Our results show that REPIC requires minimal (often no) manual intervention, and considerably reduces the burden on cryo-EM users for picker selection and particle picking. Availability: https://github.com/ccameron/REPIC .https://doi.org/10.1038/s42003-024-07045-0 |
| spellingShingle | Christopher J. F. Cameron Sebastian J. H. Seager Fred J. Sigworth Hemant D. Tagare Mark B. Gerstein REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers Communications Biology |
| title | REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers |
| title_full | REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers |
| title_fullStr | REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers |
| title_full_unstemmed | REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers |
| title_short | REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers |
| title_sort | reliable picking by consensus repic a consensus methodology for harnessing multiple cryo em particle pickers |
| url | https://doi.org/10.1038/s42003-024-07045-0 |
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