Image processing tools for the validation of CryoEM maps

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Sorzano, Carlos O. S and Vilas Prieto, José Luis and Ramírez Aportela, Erney and Krieger, J. and Hoyo, D. del and Herreros, David and Fernández Giménez, Estrella and Marchán, D. and Macías, J. R. and Sánchez, I. and Caño, L. del and Fonseca Reyna, Y. and Conesa, A. and García Mena, A. and Burguet Castell, Jordi and García Condado, J. and Méndez García, J. and Martínez, M. and Muñoz Barrutia, A. and Marabini, R. and Vargas Balbuena, Javier and Carazo, J. M. (2022) Image processing tools for the validation of CryoEM maps. Faraday discussions . ISSN 1359-6640

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Official URL: http://dx.doi.org/10.1039/d2fd00059h




Abstract

The number of maps deposited in public databases (Electron Microscopy Data Bank, EMDB) determined by cryo-electron microscopy has quickly grown in recent years. With this rapid growth, it is critical to guarantee their quality. So far, map validation has primarily focused on the agreement between maps and models. From the image processing perspective, the validation has been mostly restricted to using two half-maps and the measurement of their internal consistency. In this article, we suggest that map validation can be taken much further from the point of view of image processing if 2D classes, particles, angles, coordinates, defoci, and micrographs are also provided. We present a progressive validation scheme that qualifies a result validation status from 0 to 5 and offers three optional qualifiers (A, W, and O) that can be added. The simplest validation state is 0, while the most complete would be 5AWO. This scheme has been implemented in a website https://biocomp.cnb.csic.es/EMValidationService/ to which reconstructed maps and their ESI can be uploaded.


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© The Royal Society of Chemistry 2022.
We are thankful to Philip Baldwin, Dmitry Lyumkis, and Gabriel Lander for making their validation methods available (4.h and A.c). Javier Vargas and Jordi Burguet would like to thank the Spanish Ministry of Science and Innovation for financial support through the call 2019 Proyectos de I+D+i - RTI Tipo A (PID2019-108850RA-I00) and Arrate Muñoz Barrutia, PID2019-109820RB-I00, MCIN/AEI/10.13039/501100011033/, cofinanced by European Regional Development Fund (ERDF), "A way of making Europe.". The authors acknowledge the economic support from MICIN of the Instruct Image Processing Center (I2PC) as part of the Spanish participation in Instruct-ERIC, the European Strategic Infrastructure Project (ESFRI) in the area of Structural Biology, Grant PID2019-104757RB-I00 funded by MCIN/AEI/10.13039/501100011033/ and "ERDF A way of making Europe", by the European Union and Grant PRE2020 - 093527 funded by MCIN/AEI/ 10.13039/501100011033 and by "ESF Investing in your future". We also acknowledge support from "Comunidad Autonoma de Madrid" through Grant: S2017/BMD-3817, Instituto de Salud Carlos III (project IMPaCT-Data, exp. IMP/00019), co-funded by the European Union, European Regional Development Fund (ERDF, "A way to make Europe"), and European Union (EU) and Horizon 2020 through grants: EOSC Life (INFRAEOSC-04-2018, Proposal: 824087), HighResCells (ERC - 2018 - SyG, Proposal: 810057), IMpaCT (WIDESPREAD-03-2018 - Proposal: 857203), EOSC - Synergy (EINFRA-EOSC-5, Proposal: 857647), iNEXT-Discovery (Proposal: 871037), EnLaCES (H2020-MSCA-IF-2020, Proposal: 101024130).

Uncontrolled Keywords:Local resolution; Electron; EM; Model; Reproducibility; Orientation
Subjects:Sciences > Physics > Optics
ID Code:74067
Deposited On:05 Aug 2022 16:15
Last Modified:08 Aug 2022 07:15

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