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de Isidro-Gómez FP, Vilas JL, Losana P, Carazo JM, Sorzano COS. A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions. J Struct Biol 2024; 216:108056. [PMID: 38101554 DOI: 10.1016/j.jsb.2023.108056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/21/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular in situ observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference. Errors introduced in this step will lead to the appearance of artifacts in the tomographic reconstruction, rendering them unsuitable for the sample study. Focusing on fiducial-based acquisition strategies, this work proposes a deep-learning algorithm to detect misalignment artifacts in tomographic reconstructions by analyzing the characteristics of these fiducial markers in the tomogram. In addition, we propose an algorithm designed to detect fiducial markers in the tomogram with which to feed the classification algorithm in case the alignment algorithm does not provide the location of the markers. This open-source software is available as part of the Xmipp software package inside of the Scipion framework, and also through the command-line in the standalone version of Xmipp.
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Affiliation(s)
- F P de Isidro-Gómez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Losana
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain.
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2
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Fernandez-Gimenez E, Carazo JM, Sorzano COS. Local defocus estimation in single particle analysis in cryo-electron microscopy. J Struct Biol 2023; 215:108030. [PMID: 37758154 DOI: 10.1016/j.jsb.2023.108030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/30/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023]
Abstract
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required. A critical one is the estimation of the Contrast Transfer Function (CTF), which considers the sample defocus and aberrations of the microscope. Defocus is usually globally estimated; in this case, it is the same for all the particles in each micrograph. But proteins are ice-embedded at different heights, suggesting that defocus should be measured in a local (per particle) manner. There are four state-of-the-art programs to estimate local defocus (Gctf, Relion, CryoSPARC, and Xmipp). In this work, we have compared the results of these software packages to check whether the resolution improves. We have used the Scipion framework and developed a specific program to analyze local defocus. The results produced by different programs do not show a clear consensus using the current test datasets in this study.
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Affiliation(s)
- E Fernandez-Gimenez
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain.
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3
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Fernández-Giménez E, Martínez MM, Marabini R, Strelak D, Sánchez-García R, Carazo JM, Sorzano COS. A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis. J Struct Biol 2023; 215:108024. [PMID: 37704013 DOI: 10.1016/j.jsb.2023.108024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/22/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023]
Abstract
Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in-house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a priori.
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Affiliation(s)
- E Fernández-Giménez
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - M M Martínez
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. Autonoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - D Strelak
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - R Sánchez-García
- Department of Statistics, University of Oxford, 24-29 St Giles', Oxford OX1 3LB, United Kingdom; Astex Pharmaceuticals, 436 Cambridge Science Park, Cambridge CB4 0QA, UK
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain.
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Herreros D, Krieger JM, Fonseca Y, Conesa P, Harastani M, Vuillemot R, Hamitouche I, Serrano Gutiérrez R, Gragera M, Melero R, Jonic S, Carazo JM, Sorzano COS. Scipion Flexibility Hub: an integrative framework for advanced analysis of conformational heterogeneity in cryoEM. Acta Crystallogr D Struct Biol 2023; 79:S2059798323004497. [PMID: 37326585 DOI: 10.1107/s2059798323004497] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Understanding how structure and function meet to drive biological processes is progressively shifting the cryoEM field towards a more advanced analysis of macromolecular flexibility. Thanks to techniques such as single-particle analysis and electron tomography, it is possible to image a macromolecule in different states, information that can subsequently be extracted through advanced image-processing methods to build a richer approximation of a conformational landscape. However, the interoperability of all of these algorithms remains a challenging task that is left to users, preventing them from defining a single flexible workflow in which conformational information can be addressed by different algorithms. Therefore, in this work, a new framework integrated into Scipion is proposed called the Flexibility Hub. This framework automatically handles intercommunication between different heterogeneity software, simplifying the task of combining the software into workflows in which the quality and the amount of information extracted from flexibility analysis is maximized.
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Affiliation(s)
- D Herreros
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - J M Krieger
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - Y Fonseca
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - P Conesa
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - M Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - R Vuillemot
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - I Hamitouche
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - R Serrano Gutiérrez
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - M Gragera
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - R Melero
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - S Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - J M Carazo
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
| | - C O S Sorzano
- Centro Nacional de Biotecnologia - CSIC, Calle Darwin 3, 28049 Madrid, Spain
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5
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Herreros D, Kiska J, Ramirez E, Filipovic J, Carazo JM, Sorzano COS. ZART: A novel multiresolution reconstruction algorithm with motion-blur correction for single particle analysis. J Mol Biol 2023; 435:168088. [PMID: 37030648 DOI: 10.1016/j.jmb.2023.168088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/10/2023]
Abstract
One of the main purposes of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule thanks to the acquisition of many particle images representing different poses of the sample. By estimating the orientation of each projected particle, it is possible to recover the underlying 3D volume by multiple 3D reconstruction methods, usually working either in Fourier or in real space. However, the reconstruction from the projected images works under the assumption that all particles in the dataset correspond to the same conformation of the macromolecule. Although this requisite holds for some macromolecules, it is not true for flexible specimens, leading to motion-induced artefacts in the reconstructed CryoEM maps. In this work, we introduce a new Algebraic Reconstruction Technique called ZART, which is able to include continuous flexibility information during the reconstruction process to improve local resolution and reduce motion blurring. The conformational changes are modelled through Zernike3D polynomials. Our implementation allows for a multiresolution description of the macromolecule adapting itself to the local resolution of the reconstructed map. In addition, ZART has also proven to be a useful algorithm in cases where flexibility is not so dominant, as it improves the overall aspect of the reconstructed maps by improving their local and global resolution.
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Affiliation(s)
- D Herreros
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - J Kiska
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - E Ramirez
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - J Filipovic
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - J M Carazo
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - C O S Sorzano
- Centro Nacional de Biotecnologia-CSIC, C/ Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
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Herreros D, Lederman RR, Krieger JM, Jiménez-Moreno A, Martínez M, Myška D, Strelak D, Filipovic J, Sorzano COS, Carazo JM. Estimating conformational landscapes from Cryo-EM particles by 3D Zernike polynomials. Nat Commun 2023; 14:154. [PMID: 36631472 PMCID: PMC9832421 DOI: 10.1038/s41467-023-35791-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
The new developments in Cryo-EM Single Particle Analysis are helping us to understand how the macromolecular structure and function meet to drive biological processes. By capturing many states at the particle level, it is possible to address how macromolecules explore different conformations, information that is classically extracted through 3D classification. However, the limitations of classical approaches prevent us from fully understanding the complete conformational landscape due to the reduced number of discrete states accurately reconstructed. To characterize the whole structural spectrum of a macromolecule, we propose an extension of our Zernike3D approach, able to extract per-image continuous flexibility information directly from a particle dataset. Also, our method can be seamlessly applied to images, maps or atomic models, opening integrative possibilities. Furthermore, we introduce the ZART reconstruction algorithm, which considers the Zernike3D deformation fields to revert particle conformational changes during the reconstruction process, thus minimizing the blurring induced by molecular motions.
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Affiliation(s)
- D Herreros
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain.
| | - R R Lederman
- The Department of Statistics and Data Science, Yale University, New Haven, CT, USA
| | - J M Krieger
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - A Jiménez-Moreno
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - M Martínez
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - D Myška
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - D Strelak
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain.,Faculty of Informatics, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - J Filipovic
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200, Brno, Czech Republic
| | - C O S Sorzano
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nacional de Biotecnologia-CSIC, C/Darwin, 3, 28049, Cantoblanco, Madrid, Spain
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7
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Sorzano COS, Vilas JL, Ramírez-Aportela E, Krieger J, Del Hoyo D, Herreros D, Fernandez-Giménez E, Marchán D, Macías JR, Sánchez I, Del Caño L, Fonseca-Reyna Y, Conesa P, García-Mena A, Burguet J, García Condado J, Méndez García J, Martínez M, Muñoz-Barrutia A, Marabini R, Vargas J, Carazo JM. Image processing tools for the validation of CryoEM maps. Faraday Discuss 2022; 240:210-227. [PMID: 35861059 DOI: 10.1039/d2fd00059h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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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Affiliation(s)
- C O S Sorzano
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J L Vilas
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | | | - J Krieger
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - D Del Hoyo
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - D Herreros
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | | | - D Marchán
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J R Macías
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - I Sánchez
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - L Del Caño
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - Y Fonseca-Reyna
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - P Conesa
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - A García-Mena
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - J Burguet
- Depto. de Óptica, Univ. Complutense de Madrid, Pl. Ciencias, 1, 28040, Madrid, Spain
| | - J García Condado
- Biocruces Bizkaia Instituto Investigación Sanitaria, Cruces Plaza, 48903, Barakaldo, Bizkaia, Spain
| | | | - M Martínez
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
| | - A Muñoz-Barrutia
- Univ. Carlos III de Madrid, Avda. de la Universidad 30, 28911, Leganés, Madrid, Spain
| | - R Marabini
- Escuela Politécnica Superior, Univ. Autónoma de Madrid, CSIC, C. Francisco Tomás y Valiente, 11, 28049, Madrid, Spain
| | - J Vargas
- Depto. de Óptica, Univ. Complutense de Madrid, Pl. Ciencias, 1, 28040, Madrid, Spain
| | - J M Carazo
- Natl. Center of Biotechnology, CSIC, c/Darwin, 3, 28049, Madrid, Spain.
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Jiménez de la Morena J, Conesa P, Fonseca YC, de Isidro-Gómez FP, Herreros D, Fernández-Giménez E, Strelak D, Moebel E, Buchholz TO, Jug F, Martinez-Sanchez A, Harastani M, Jonic S, Conesa JJ, Cuervo A, Losana P, Sánchez I, Iceta M, Del Cano L, Gragera M, Melero R, Sharov G, Castaño-Díez D, Koster A, Piccirillo JG, Vilas JL, Otón J, Marabini R, Sorzano COS, Carazo JM. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. J Struct Biol 2022; 214:107872. [PMID: 35660516 PMCID: PMC7613607 DOI: 10.1016/j.jsb.2022.107872] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/25/2022]
Abstract
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline. The Scipion framework, originally developed for SPA (de la Rosa-Trevín et al., 2016), has a generic python workflow engine that gives it the versatility to be extended to other fields, as demonstrated for model building (Martínez et al., 2020). In this article, we provide an extension of Scipion based on a set of tomography plugins (referred to as ScipionTomo hereafter), with a similar purpose: to allow users to be focused on the data processing and analysis instead of having to deal with multiple software installation issues and the inconvenience of switching from one to another, converting metadata files, managing possible incompatibilities, scripting (writing a simple program in a language that the computer must convert to machine language each time the program is run), etcetera. Additionally, having all the software available in an integrated platform allows comparing the results of different algorithms trying to solve the same problem. In this way, the commonalities and differences between estimated parameters shed light on which results can be more trusted than others. ScipionTomo is developed by a collaborative multidisciplinary team composed of Scipion team engineers, structural biologists, and in some cases, the developers whose software packages have been integrated. It is open to anyone in the field willing to contribute to this project. The result is a framework extension that combines the acquired knowledge of Scipion developers in close collaboration with third-party developers, and the on-demand design of functionalities requested by beta testers applying this solution to actual biological problems.
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Affiliation(s)
| | - P Conesa
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - Y C Fonseca
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - D Herreros
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | | | - D Strelak
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Masaryk University, Brno, Czech Republic
| | - E Moebel
- Inria Rennes - Bretagne Atlantique, Rennes
| | - T O Buchholz
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Center for Systems Biology Dresden (CSBD), Germany
| | - F Jug
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Germany; Fondazione Human Technopole, Milan, Italy
| | - A Martinez-Sanchez
- University of Oviedo, Department of Computer Sciences, Oviedo, Spain; Health Research Institute of Asturias (ISPA), Oviedo, Spain
| | - M Harastani
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - S Jonic
- IMPMC-UMR 7590 CNRS, Sorbonne Université, MNHN, Paris, France
| | - J J Conesa
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - A Cuervo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - P Losana
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - I Sánchez
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Iceta
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - L Del Cano
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - M Gragera
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - R Melero
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - G Sharov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - D Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland
| | - A Koster
- University of Leiden, Ultrastructural and molecular imaging, Leiden, The Netherlands
| | - J G Piccirillo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J L Vilas
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J Otón
- Alba Synchrotron - CELLS (ICTS), Barcelona, Spain
| | - R Marabini
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain; Superior Polytechnic School. Univ. Autónoma of Madrid. Madrid, Spain
| | - C O S Sorzano
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
| | - J M Carazo
- National Center of Biotechnology (CNB-CSIC), Madrid, Spain
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9
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Sorzano COS, Carazo JM. Cryo-Electron Microscopy: the field of 1,000 + methods. J Struct Biol 2022; 214:107861. [PMID: 35568276 DOI: 10.1016/j.jsb.2022.107861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 01/18/2023]
Abstract
Cryo-Electron Microscopy (CryoEM) is currently a well-established method to elucidate a biological macromolecule's three-dimensional (3D) structure. Its success is due to technological and methodological advances in several fronts: sample preparation, electron optics and detection, image acquisition, image processing, and map interpretation. The first methods started in the late 1960s and, since then, new methods on all fronts have continuously been published, maturating the field as we know it now. In terms of publications, we can distinguish several periods, witnessing a substantial acceleration of methodological publications in recent years, pointing out to an increased interest in the domain. On the other hand, this accelerated increase of methods development may confuse practitioners about which method they should be using (and how) and highlight the importance of paying attention to establishing best practices for methods reporting and usage. In this paper, we analyze the trends identified in over 1,000 methodological papers. Our focus is primarily on computational image processing methods. However, our list also covers some aspects of sample preparation and image acquisition. Several interesting ideas stem out from this study: 1) Single Particle Analysis (SPA) has largely accelerated in the last decade and sample preparation methods in the last five years; 2) Electron Tomography is not yet in a rapidly growing phase, but it is foreseeable that it will soon be; 3) the work horses of SPA are 3D classification, 3D reconstruction, and 3D alignment, and there have been many papers on these topics, which are not considered to be solved yet, but ever improving; and 4) since the resolution revolution, atomic modelling has also caught on as a hot topic.
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Affiliation(s)
- C O S Sorzano
- Natl. Center of Biotechnology, CSIC. c/Darwin, 3. Campus Univ. Autónoma de Madrid. 28049 Madrid, Spain
| | - J M Carazo
- Natl. Center of Biotechnology, CSIC. c/Darwin, 3. Campus Univ. Autónoma de Madrid. 28049 Madrid, Spain
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Sorzano COS, Jiménez-Moreno A, Maluenda D, Martínez M, Ramírez-Aportela E, Krieger J, Melero R, Cuervo A, Conesa J, Filipovic J, Conesa P, del Caño L, Fonseca YC, Jiménez-de la Morena J, Losana P, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro-Gómez FP, Herreros D, Vilas JL, Marabini R, Carazo JM. On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy. Acta Crystallogr D Struct Biol 2022; 78:410-423. [PMID: 35362465 PMCID: PMC8972802 DOI: 10.1107/s2059798322001978] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 02/18/2022] [Indexed: 12/05/2022] Open
Abstract
Single-particle analysis (SPA) by cryo-electron microscopy comprises the estimation of many parameters along its image-processing pipeline. Overfitting observed in SPA is normally due to misestimated parameters, and the only way to identify these is by comparing the estimates of multiple algorithms or, at least, multiple executions of the same algorithm. Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands of macromolecules that are assumed to be structurally identical are combined into a single 3D map representing the Coulomb potential of the macromolecule under study. This article discusses possible caveats along the image-processing path and how to avoid them to obtain a reliable 3D structure. Some of these problems are very well known in the community. These may be referred to as sample-related (such as specimen denaturation at interfaces or non-uniform projection geometry leading to underrepresented projection directions). The rest are related to the algorithms used. While some have been discussed in depth in the literature, such as the use of an incorrect initial volume, others have received much less attention. However, they are fundamental in any data-analysis approach. Chiefly among them, instabilities in estimating many of the key parameters that are required for a correct 3D reconstruction that occur all along the processing workflow are referred to, which may significantly affect the reliability of the whole process. In the field, the term overfitting has been coined to refer to some particular kinds of artifacts. It is argued that overfitting is a statistical bias in key parameter-estimation steps in the 3D reconstruction process, including intrinsic algorithmic bias. It is also shown that common tools (Fourier shell correlation) and strategies (gold standard) that are normally used to detect or prevent overfitting do not fully protect against it. Alternatively, it is proposed that detecting the bias that leads to overfitting is much easier when addressed at the level of parameter estimation, rather than detecting it once the particle images have been combined into a 3D map. Comparing the results from multiple algorithms (or at least, independent executions of the same algorithm) can detect parameter bias. These multiple executions could then be averaged to give a lower variance estimate of the underlying parameters.
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11
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Jiménez-Moreno A, Del Caño L, Martínez M, Ramírez-Aportela E, Cuervo A, Melero R, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro-Gómez FP, Herreros D, Conesa P, Fonseca Y, Maluenda D, Jiménez de la Morena J, Macías JR, Losana P, Marabini R, Carazo JM, Sorzano COS. Cryo-EM and Single-Particle Analysis with Scipion. J Vis Exp 2021. [PMID: 34125107 DOI: 10.3791/62261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Cryo-electron microscopy has become one of the most important tools in biological research to reveal the structural information of macromolecules at near-atomic resolution. In single-particle analysis, the vitrified sample is imaged by an electron beam and the detectors at the end of the microscope column produce movies of that sample. These movies contain thousands of images of identical particles in random orientations. The data need to go through an image processing workflow with multiple steps to obtain the final 3D reconstructed volume. The goal of the image processing workflow is to identify the acquisition parameters to be able to reconstruct the specimen under study. Scipion provides all the tools to create this workflow using several image processing packages in an integrative framework, also allowing the traceability of the results. In this article the whole image processing workflow in Scipion is presented and discussed with data coming from a real test case, giving all the details necessary to go from the movies obtained by the microscope to a high resolution final 3D reconstruction. Also, the power of using consensus tools that allow combining methods, and confirming results along every step of the workflow, improving the accuracy of the obtained results, is discussed.
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Affiliation(s)
- A Jiménez-Moreno
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - L Del Caño
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - M Martínez
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | | | - A Cuervo
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - R Melero
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - R Sánchez-García
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - D Strelak
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid; Faculty of Informatics, Masaryk University; Institute of Computer Science, Masaryk University
| | | | | | - D Herreros
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - P Conesa
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - Y Fonseca
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - D Maluenda
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid;
| | | | - J R Macías
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - P Losana
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - R Marabini
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - J M Carazo
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid
| | - C O S Sorzano
- Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid; Campus Urbanización Montepríncipe, Universidad San Pablo CEU
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12
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Jiménez-Moreno A, Střelák D, Filipovič J, Carazo JM, Sorzano COS. DeepAlign, a 3D alignment method based on regionalized deep learning for Cryo-EM. J Struct Biol 2021; 213:107712. [PMID: 33676034 DOI: 10.1016/j.jsb.2021.107712] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 02/02/2021] [Accepted: 02/21/2021] [Indexed: 02/02/2023]
Abstract
Cryo Electron Microscopy (Cryo-EM) is currently one of the main tools to reveal the structural information of biological specimens at high resolution. Despite the great development of the techniques involved to solve the biological structures with Cryo-EM in the last years, the reconstructed 3D maps can present lower resolution due to errors committed while processing the information acquired by the microscope. One of the main problems comes from the 3D alignment step, which is an error-prone part of the reconstruction workflow due to the very low signal-to-noise ratio (SNR) common in Cryo-EM imaging. In fact, as we will show in this work, it is not unusual to find a disagreement in the alignment parameters in approximately 20-40% of the processed images, when outputs of different alignment algorithms are compared. In this work, we present a novel method to align sets of single particle images in the 3D space, called DeepAlign. Our proposal is based on deep learning networks that have been successfully used in plenty of problems in image classification. Specifically, we propose to design several deep neural networks on a regionalized basis to classify the particle images in sub-regions and, then, make a refinement of the 3D alignment parameters only inside that sub-region. We show that this method results in accurately aligned images, improving the Fourier shell correlation (FSC) resolution obtained with other state-of-the-art methods while decreasing computational time.
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Affiliation(s)
- A Jiménez-Moreno
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - D Střelák
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Faculty of Informatics, Masaryk University, Botanická 68a, 662 00 Brno, Czech Republic; Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - J Filipovič
- Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain.
| | - C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
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13
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Kazemi M, Sorzano COS, Carazo JM, Georges AD, Abrishami V, Vargas J. ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions. Prog Biophys Mol Biol 2021; 164:92-100. [PMID: 33450244 DOI: 10.1016/j.pbiomolbio.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 11/27/2022]
Abstract
Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.
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Affiliation(s)
- M Kazemi
- Dep. of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - A des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA; Dept. of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - V Abrishami
- Laboratory of Structural Biology, Helsinki Institute of Life Science HiLIFE, Finland
| | - J Vargas
- Departamento de Optica, Universidad Complutense de Madrid, Avda. Computense s/n, Ciudad Universitaria, 28040, Madrid, Spain; Department of Anatomy and Cell Biology, McGill University, 3640, Rue University, Montréal, QC, H3A 0C7, Canada.
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14
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Sorzano COS, Semchonok D, Lin SC, Lo YC, Vilas JL, Jiménez-Moreno A, Gragera M, Vacca S, Maluenda D, Martínez M, Ramírez-Aportela E, Melero R, Cuervo A, Conesa JJ, Conesa P, Losana P, Caño LD, de la Morena JJ, Fonseca YC, Sánchez-García R, Strelak D, Fernández-Giménez E, de Isidro F, Herreros D, Kastritis PL, Marabini R, Bruce BD, Carazo JM. Algorithmic robustness to preferred orientations in single particle analysis by CryoEM. J Struct Biol 2021; 213:107695. [PMID: 33421545 DOI: 10.1016/j.jsb.2020.107695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/18/2020] [Accepted: 12/24/2020] [Indexed: 01/30/2023]
Abstract
The presence of preferred orientations in single particle analysis (SPA) by cryo-Electron Microscopy (cryoEM) is currently one of the hurdles preventing many structural analyses from yielding high-resolution structures. Although the existence of preferred orientations is mostly related to the grid preparation, in this technical note, we show that some image processing algorithms used for angular assignment and three-dimensional (3D) reconstruction are more robust than others to these detrimental conditions. We exemplify this argument with three different data sets in which the presence of preferred orientations hindered achieving a 3D reconstruction without artifacts or, even worse, a 3D reconstruction could never be achieved.
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Affiliation(s)
- C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain.
| | - D Semchonok
- ZIK HALOMEM & Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - S-C Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Y-C Lo
- Dept. Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - J L Vilas
- Dept. of Biomedical Engineering, Yale University, New Haven, United States
| | - A Jiménez-Moreno
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - M Gragera
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - S Vacca
- Dept. of Biochemistry, Univ. Zurich, Winterthurerstr. 190, CH-8057 Zurich, Switzerland
| | - D Maluenda
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martínez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramírez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - A Cuervo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J J Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Losana
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - L Del Caño
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Jiménez de la Morena
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Y C Fonseca
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Sánchez-García
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - D Strelak
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Fernández-Giménez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - F de Isidro
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - D Herreros
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P L Kastritis
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Escuela Politecnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - B D Bruce
- Dept. Biochemistry & Cellular and Molecular Biology, Univ. Tennessee Knoxville, Knoxville, TN 37996, United States
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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15
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Sorzano COS, de Isidro-Gómez F, Fernández-Giménez E, Herreros D, Marco S, Carazo JM, Messaoudi C. Improvements on marker-free images alignment for electron tomography. J Struct Biol X 2020; 4:100037. [PMID: 33024955 PMCID: PMC7527754 DOI: 10.1016/j.yjsbx.2020.100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Electron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.
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Affiliation(s)
- C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Aut'onoma, 28049 Cantoblanco, Madrid, Spain
| | - F de Isidro-Gómez
- Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Aut'onoma, 28049 Cantoblanco, Madrid, Spain
| | - E Fernández-Giménez
- Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Aut'onoma, 28049 Cantoblanco, Madrid, Spain
| | - D Herreros
- Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Aut'onoma, 28049 Cantoblanco, Madrid, Spain
| | - S Marco
- Institite Curie, 110 Avenue de Bures, 91440 Bures-sur-Yvette, France
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Aut'onoma, 28049 Cantoblanco, Madrid, Spain
| | - C Messaoudi
- Institite Curie, 110 Avenue de Bures, 91440 Bures-sur-Yvette, France
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16
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Vilas JL, Heymann JB, Tagare HD, Ramirez-Aportela E, Carazo JM, Sorzano C. Local resolution estimates of cryoEM reconstructions. Curr Opin Struct Biol 2020; 64:74-78. [PMID: 32645578 DOI: 10.1016/j.sbi.2020.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/28/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022]
Abstract
The field of cryoEM has quickly advanced in last years with the new biochemical, technological, methodological and computational developments. It has allowed significant progresses in Structural Biology, typically reaching quasi-atomic resolutions in the reconstructed maps. However, this rapid advance has also generated new questions relevant to resolution estimates. The global resolution metrics and their criteria have been deeply discussed in the last decade, but despite that, it remains as an important issue in the field. Recently, the introduction of local resolution measurements has changed how cryoEM reconstructions are interpreted, providing information about the existence of heterogeneity, flexibility, and angular assignment errors, and using it as a tool to aid in modeling. In this review we revisit the concept of local resolution and the different algorithms in the current state of the art. However, the concept of local resolution is not uniquely defined, and each implementation measures different features. This may lead to inappropriate interpretation of local resolution maps. Hence, a set of good practices is provided in this review to avoid misleading and over-interpretation of the reconstructions.
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Affiliation(s)
- J L Vilas
- Department of Biomedical Engineering, Yale University, New Haven, United States
| | - J B Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - H D Tagare
- Department of Biomedical Engineering, Yale University, New Haven, United States
| | - E Ramirez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Cos Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo-CEU, Campus Urb. Monteprincipe, 28668 Boadilla del Monte, Madrid, Spain.
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Segura J, Sanchez-Garcia R, Sorzano COS, Carazo JM. 3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations. Bioinformatics 2020; 35:3512-3513. [PMID: 30768147 PMCID: PMC6748749 DOI: 10.1093/bioinformatics/btz118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 12/17/2018] [Accepted: 02/13/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Many diseases are associated to single nucleotide polymorphisms that affect critical regions of proteins as binding sites or post translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases. RESULTS A new version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences and a protein-protein interaction viewer to display protein annotations at network level. AVAILABILITY AND IMPLEMENTATION The web server is available at https://3dbionotes.cnb.csic.es. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, C/ Darwin nº 3, Campus of Cantoblanco, 28049 Madrid, Spain.
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Affiliation(s)
- Joan Segura
- Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, Madrid, Spain
| | - Ruben Sanchez-Garcia
- Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, Madrid, Spain
| | - C O S Sorzano
- Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, Madrid, Spain
| | - J M Carazo
- Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)/Instruct Image Processing Centre, Madrid, Spain
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18
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Sanchez-Garcia R, Segura J, Maluenda D, Sorzano COS, Carazo JM. MicrographCleaner: A python package for cryo-EM micrograph cleaning using deep learning. J Struct Biol 2020; 210:107498. [PMID: 32276087 DOI: 10.1016/j.jsb.2020.107498] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/03/2020] [Accepted: 03/26/2020] [Indexed: 01/21/2023]
Abstract
Cryo-EM Single Particle Analysis workflows require tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for automatic particle picking tend to suffer from high false-positive rates, hampering the reconstruction process. One common cause of this problem is the presence of carbon and different types of high-contrast contaminations. In order to overcome this limitation, we have developed MicrographCleaner, a deep learning package designed to discriminate, in an automated fashion, between regions of micrographs which are suitable for particle picking, and those which are not. MicrographCleaner implements a U-net-like deep learning model trained on a manually curated dataset compiled from over five hundred micrographs. The benchmarking, carried out on approximately one hundred independent micrographs, shows that MicrographCleaner is a very efficient approach for micrograph preprocessing. MicrographCleaner (micrograph_cleaner_em) package is available at PyPI and Anaconda Cloud and also as a Scipion/Xmipp protocol. Source code is available at https://github.com/rsanchezgarc/micrograph_cleaner_em.
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Affiliation(s)
- Ruben Sanchez-Garcia
- National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/ Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain.
| | - Joan Segura
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - David Maluenda
- National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/ Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain
| | - C O S Sorzano
- National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/ Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain
| | - J M Carazo
- National Center of Biotechnology (CSIC)/Instruct Image Processing Center, C/ Darwin n° 3, Campus of Cantoblanco, 28049 Madrid, Spain
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19
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Martínez M, Jiménez-Moreno A, Maluenda D, Ramírez-Aportela E, Melero R, Cuervo A, Conesa P, Del Caño L, Fonseca YC, Sánchez-García R, Strelak D, Conesa JJ, Fernández-Giménez E, de Isidro F, Sorzano COS, Carazo JM, Marabini R. Integration of Cryo-EM Model Building Software in Scipion. J Chem Inf Model 2020; 60:2533-2540. [PMID: 31994878 DOI: 10.1021/acs.jcim.9b01032] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Advances in cryo-electron microscopy (cryo-EM) have made it possible to obtain structures of large biological macromolecules at near-atomic resolution. This "resolution revolution" has encouraged the use and development of modeling tools able to produce high-quality atomic models from cryo-EM density maps. Unfortunately, many practical problems appear when combining different packages in the same processing workflow, which make difficult the use of these tools by non-experts and, therefore, reduce their utility. We present here a major extension of the image processing framework Scipion that provides inter-package integration in the model building area and full tracking of the complete workflow, from image processing to structure validation.
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Affiliation(s)
- M Martínez
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | | | - D Maluenda
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | | | - R Melero
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - A Cuervo
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - P Conesa
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - L Del Caño
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | | | | | - D Strelak
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain.,Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
| | - J J Conesa
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | | | | | | | - J M Carazo
- CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
| | - R Marabini
- Escuela Politécnica, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 11, 28049 Madrid, Spain
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20
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Vilas JL, Vargas J, Martinez M, Ramirez-Aportela E, Melero R, Jimenez-Moreno A, Garduño E, Conesa P, Marabini R, Maluenda D, Carazo JM, Sorzano COS. Re-examining the spectra of macromolecules. Current practice of spectral quasi B-factor flattening. J Struct Biol 2020; 209:107447. [PMID: 31911170 DOI: 10.1016/j.jsb.2020.107447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 12/29/2019] [Accepted: 01/01/2020] [Indexed: 11/24/2022]
Abstract
The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accomplish this enhancement is by means of the so-called B-factor correction, which applies a global filter to boost high frequencies with some dampening considerations related to noise amplification. The results are maps with a better visual aspect and a quasiflat spectrum at medium and high frequencies. This practice is so widespread that most map depositions in the Electron Microscopy Data Base (EMDB) only contain sharpened maps. Here, the use in cryoEM of global B-factor corrections is theoretically and experimentally analyzed. Results clearly illustrate that protein spectra present a falloff. Thus, spectral quasi-flattening may produce protein spectra with distortions when compared with experimental ones, this fact, combined with the practice of reporting only sharpened maps, generates a sub-optimal situation in terms of data preservation, reuse and reproducibility. Now that the field is more advanced, we put forward two suggestions: (1) to use methods which keep more faithfully the original experimental signal properties of macromolecules when "enhancing" the map, and (2) to further stress the need to deposit the original experimental maps without any postprocessing or sharpening, not only the enhanced maps. In the absence of access to these original maps data is lost, preventing their future analysis with new methods.
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Affiliation(s)
- J L Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Vargas
- Dept. Anatomy and Cell Biology, McGill Univ., Montreal, Canada
| | - M Martinez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramirez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jimenez-Moreno
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Garduño
- Department of Computer Science, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, 04510 Mexico City, Mexico
| | - P Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Escuela Politecnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - D Maluenda
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Monteprincipe, 28668 Boadilla del Monte, Madrid, Spain.
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21
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Vilas JL, Oton J, Messaoudi C, Melero R, Conesa P, Ramirez-Aportela E, Mota J, Martinez M, Jimenez A, Marabini R, Carazo JM, Vargas J, Sorzano COS. Measurement of local resolution in electron tomography. J Struct Biol X 2019; 4:100016. [PMID: 32647820 PMCID: PMC7337044 DOI: 10.1016/j.yjsbx.2019.100016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/13/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023]
Abstract
Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number. However, it is known that tomogram quality is spatially variant. Still, up to our knowledge, a method to estimate local quality metrics in tomography is lacking. This work introduces MonoTomo, a method developed to estimate locally in a tomogram the highest reliable frequency component, expressed as a form of local resolution. The fundamentals lie in a local analysis of the density map via monogenic signals, which, in analogy to MonoRes, allows for local estimations. Results with experimental data show that the local resolution range that MonoTomo casts agrees with reported resolution values for experimental data sets, with the advantage of providing a local estimation. A range of applications of MonoTomo are suggested for further exploration.
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Affiliation(s)
- J L Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Oton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - C Messaoudi
- U1196, Institut Curie, INSERM, PSL Reseach University, F-91405 Orsay, France
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramirez-Aportela
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Mota
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martinez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jimenez
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - J Vargas
- Dept. Anatomy and Cell Biology, McGill Univ., Montreal, Canada
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain.,Univ. San Pablo - CEU, Campus Urb. Monteprincipe, 28668 Boadilla del Monte, Madrid, Spain
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22
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Sanchez-Garcia R, Sorzano COS, Carazo JM, Segura J. BIPSPI: a method for the prediction of partner-specific protein-protein interfaces. Bioinformatics 2019; 35:470-477. [PMID: 30020406 PMCID: PMC6361243 DOI: 10.1093/bioinformatics/bty647] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/17/2018] [Indexed: 11/15/2022] Open
Abstract
Motivation Protein-Protein Interactions (PPI) are essentials for most cellular processes and thus, unveiling how proteins interact is a crucial question that can be better understood by identifying which residues are responsible for the interaction. Computational approaches are orders of magnitude cheaper and faster than experimental ones, leading to proliferation of multiple methods aimed to predict which residues belong to the interface of an interaction. Results We present BIPSPI, a new machine learning-based method for the prediction of partner-specific PPI sites. Contrary to most binding site prediction methods, the proposed approach takes into account a pair of interacting proteins rather than a single one in order to predict partner-specific binding sites. BIPSPI has been trained employing sequence-based and structural features from both protein partners of each complex compiled in the Protein-Protein Docking Benchmark version 5.0 and in an additional set independently compiled. Also, a version trained only on sequences has been developed. The performance of our approach has been assessed by a leave-one-out cross-validation over different benchmarks, outperforming state-of-the-art methods. Availability and implementation BIPSPI web server is freely available at http://bipspi.cnb.csic.es. BIPSPI code is available at https://github.com/bioinsilico/BIPSPI. Docker image is available at https://hub.docker.com/r/bioinsilico/bipspi/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruben Sanchez-Garcia
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid, Spain
| | - C O S Sorzano
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid, Spain
| | - J M Carazo
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid, Spain
| | - Joan Segura
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid, Spain
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23
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Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García C, Strelak D, Melero R, Marabini R, Carazo JM, Sorzano COS. Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion. Acta Crystallogr D Struct Biol 2019; 75:882-894. [PMID: 31588920 PMCID: PMC6778851 DOI: 10.1107/s2059798319011860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023] Open
Abstract
Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.
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Affiliation(s)
- D. Maluenda
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - T. Majtner
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Horvath
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. L. Vilas
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - A. Jiménez-Moreno
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. Mota
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | | | - R. Sánchez-García
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Conesa
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - L. del Caño
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Rancel
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Fonseca
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - M. Martínez
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - G. Sharov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, England
| | | | - D. Strelak
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Melero
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Marabini
- Universidad Autónoma de Madrid, Madrid, Spain
| | - J. M. Carazo
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - C. O. S. Sorzano
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
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24
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Sorzano COS, Jiménez A, Mota J, Vilas JL, Maluenda D, Martínez M, Ramírez-Aportela E, Majtner T, Segura J, Sánchez-García R, Rancel Y, del Caño L, Conesa P, Melero R, Jonic S, Vargas J, Cazals F, Freyberg Z, Krieger J, Bahar I, Marabini R, Carazo JM. Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy. Acta Crystallogr F Struct Biol Commun 2019; 75:19-32. [PMID: 30605122 PMCID: PMC6317454 DOI: 10.1107/s2053230x18015108] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/26/2018] [Indexed: 11/10/2022] Open
Abstract
Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.
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Affiliation(s)
| | - A. Jiménez
- National Center of Biotechnology (CSIC), Spain
| | - J. Mota
- National Center of Biotechnology (CSIC), Spain
| | - J. L. Vilas
- National Center of Biotechnology (CSIC), Spain
| | - D. Maluenda
- National Center of Biotechnology (CSIC), Spain
| | - M. Martínez
- National Center of Biotechnology (CSIC), Spain
| | | | - T. Majtner
- National Center of Biotechnology (CSIC), Spain
| | - J. Segura
- National Center of Biotechnology (CSIC), Spain
| | | | - Y. Rancel
- National Center of Biotechnology (CSIC), Spain
| | - L. del Caño
- National Center of Biotechnology (CSIC), Spain
| | - P. Conesa
- National Center of Biotechnology (CSIC), Spain
| | - R. Melero
- National Center of Biotechnology (CSIC), Spain
| | - S. Jonic
- Sorbonne Université, UMR CNRS 7590, Muséum National d’Histoire Naturelle, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | | | - F. Cazals
- Inria Sophia Antipolis – Méditerranée, France
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25
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Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, Del Cano L, Jiménez A, Martínez M, Melero R, Majtner T, Maluenda D, Mota J, Rancel Y, Ramírez-Aportela E, Vilas JL, Carroni M, Fleischmann S, Lindahl E, Ashton AW, Basham M, Clare DK, Savage K, Siebert CA, Sharov GG, Sorzano COS, Conesa P, Carazo JM. Using Scipion for stream image processing at Cryo-EM facilities. J Struct Biol 2018; 204:457-463. [PMID: 30296492 PMCID: PMC6303188 DOI: 10.1016/j.jsb.2018.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Abstract
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.
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Affiliation(s)
- J Gómez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - J M de la Rosa-Trevín
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - L Del Cano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jiménez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martínez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - D Maluenda
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J Mota
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - Y Rancel
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramírez-Aportela
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - S Fleischmann
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - E Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - A W Ashton
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - M Basham
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - D K Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - K Savage
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - C A Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - G G Sharov
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, United Kingdom
| | - C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
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26
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Marabini R, Kazemi M, Sorzano COS, Carazo JM. Map challenge: Analysis using a pair comparison method based on Fourier shell correlation. J Struct Biol 2018; 204:527-542. [PMID: 30273658 DOI: 10.1016/j.jsb.2018.09.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 12/22/2022]
Abstract
This document presents the analysis performed over the Map Challenge dataset using a new algorithm which we refer to as Pair Comparison Method. The new algorithm, which is described in detail in the text, is able to sort reconstructions based on a figure of merit and assigns a level of significance to the sorting. That is, it shows how likely the sorting is due to chance or if it reflects real differences.
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Affiliation(s)
- R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - M Kazemi
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, The University of Melbourne, VIC 3010, Australia
| | - C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
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27
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Segura J, Sanchez-Garcia R, Martinez M, Cuenca-Alba J, Tabas-Madrid D, Sorzano COS, Carazo JM. 3DBIONOTES v2.0: a web server for the automatic annotation of macromolecular structures. Bioinformatics 2018; 33:3655-3657. [PMID: 28961691 PMCID: PMC5870569 DOI: 10.1093/bioinformatics/btx483] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/27/2017] [Indexed: 11/13/2022] Open
Abstract
Motivation Complementing structural information with biochemical and biomedical annotations is a powerful approach to explore the biological function of macromolecular complexes. However, currently the compilation of annotations and structural data is a feature only available for those structures that have been released as entries to the Protein Data Bank. Results To help researchers in assessing the consistency between structures and biological annotations for structural models not deposited in databases, we present 3DBIONOTES v2.0, a web application designed for the automatic annotation of biochemical and biomedical information onto macromolecular structural models determined by any experimental or computational technique. Availability and implementation The web server is available at http://3dbionotes-ws.cnb.csic.es. Contact jsegura@cnb.csic.es. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joan Segura
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - Ruben Sanchez-Garcia
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - Marta Martinez
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - Jesus Cuenca-Alba
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - Daniel Tabas-Madrid
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - C O S Sorzano
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
| | - J M Carazo
- GN7 of the Spanish National Institute for Bioinformatics (INB), Biocomputing Unit, National Center of Biotechnology (CSIC), Instruct Image Processing Center, Madrid 28049, Spain
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de la Rosa-Trevín JM, Gómez-Blanco J, Conesa P, Rancel Y, del Cano L, Arranz R, Chichón FJ, Martín-Benito J, Carroni M, Fleichman S, Lindahl E, Basham M, Clare DK, Savage K, Siebert CA, Ashton AW, Marabini R, Sorzano COS, Carazo JM. Using Scipion for stream image processing at cryo-EM facilities. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318098380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sorzano COS, Fernández-Giménez E, Peredo-Robinson V, Vargas J, Majtner T, Caffarena G, Otón J, Vilas JL, de la Rosa-Trevín JM, Melero R, Gómez-Blanco J, Cuenca J, Del Cano L, Conesa P, Marabini R, Carazo JM. Blind estimation of DED camera gain in Electron Microscopy. J Struct Biol 2018; 203:90-93. [PMID: 29551714 DOI: 10.1016/j.jsb.2018.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 12/17/2022]
Abstract
The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image. The algorithm does not need any other input than the DED movie itself, being capable of providing an estimate of the camera gain image, helping to identify dead pixels and cases of incorrectly calibrated cameras. We propose the algorithm to be used either to validate the experimentally acquired gain image (for instance, to follow its possible change over time) or to verify that there is no residual gain image after experimentally correcting for the camera gain. We show results for a number of DED camera models currently in use (DE, Falcon II, Falcon 3, and K2).
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Affiliation(s)
- C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
| | - E Fernández-Giménez
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - V Peredo-Robinson
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Vargas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - G Caffarena
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - J Otón
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | | | - R Melero
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Gómez-Blanco
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Cuenca
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - L Del Cano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
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Vargas J, Franken E, Sorzano COS, Gomez-Blanco J, Schoenmakers R, Koster AJ, Carazo JM. Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope. J Struct Biol 2016; 196:515-524. [PMID: 27725258 DOI: 10.1016/j.jsb.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 11/19/2022]
Abstract
Automatic or semiautomatic data collection approaches on a transmission electron microscope (TEM) for Single Particle Analysis, capable of acquiring large datasets composed of only high quality images, are of great importance to obtain 3D density maps with the highest resolution possible. Typically, this task is performed by an experienced microscopist, who manually decides to keep or discard images according to subjective criteria. Therefore, this methodology is slow, intensive in human work and subjective. In this work, we propose a method to automatically or semiautomatically perform this image selection task. The approach is based on some simple, fast and effective image quality descriptors, which can be computed during acquisition, to characterize foil-hole and data images. The proposed approach has been used to evaluate the quality of different datasets consisting of foil-hole and data images obtained with a FEI Titan Krios electron microscope. The results show that the proposed method is very effective evaluating the quality of foil-hole and data images, as well as predicting the quality of the data images from the foil-hole images.
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Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain.
| | - E Franken
- FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
| | - J Gomez-Blanco
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
| | - R Schoenmakers
- FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - A J Koster
- Koster Lab, Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
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31
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Sorzano COS, Martín-Ramos A, Prieto F, Melero R, Martín-Benito J, Jonic S, Navas-Calvente J, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo JM. Local analysis of strains and rotations for macromolecular electron microscopy maps. J Struct Biol 2016; 195:123-8. [PMID: 27102900 DOI: 10.1016/j.jsb.2016.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/01/2016] [Accepted: 04/06/2016] [Indexed: 01/23/2023]
Abstract
Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the different areas of the protein. The analysis of these local deformations may reveal important insight into the way proteins perform their tasks. In this paper we introduce a method to perform this kind of local analysis using Electron Microscopy volumes in a fully objective and automatic manner. For doing so, we exploit the continuous nature of the result of an elastic image registration using B-splines as its basis functions. We show that the results obtained by the new automatic method are consistent with previous observations on these macromolecules.
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Affiliation(s)
- C O S Sorzano
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain; Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain.
| | - A Martín-Ramos
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - F Prieto
- Univ. San Pablo - CEU, Campus Urb. Montepríncipe, 28668 Boadilla del Monte, Madrid, Spain
| | - R Melero
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Martín-Benito
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - S Jonic
- IMPMC, Sorbonne Universités - CNRS UMR 7590, UPMC University Paris 6, MNHN, IRDUMR206, 75005 Paris, France
| | - J Navas-Calvente
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Vargas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J Otón
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - V Abrishami
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | | | - J Gómez-Blanco
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Univ. Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Centro Nac. Biotecnología (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain
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Jonić S, Vargas J, Melero R, Gómez-Blanco J, Carazo JM, Sorzano COS. Denoising of high-resolution single-particle electron-microscopy density maps by their approximation using three-dimensional Gaussian functions. J Struct Biol 2016; 194:423-33. [PMID: 27085420 DOI: 10.1016/j.jsb.2016.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 12/22/2022]
Abstract
Cryo-electron microscopy (cryo-EM) of frozen-hydrated preparations of isolated macromolecular complexes is the method of choice to obtain the structure of complexes that cannot be easily studied by other experimental methods due to their flexibility or large size. An increasing number of macromolecular structures are currently being obtained at subnanometer resolution but the interpretation of structural details in such EM-derived maps is often difficult because of noise at these high-frequency signal components that reduces their contrast. In this paper, we show that the method for EM density-map approximation using Gaussian functions can be used for denoising of single-particle EM maps of high (typically subnanometer) resolution. We show its denoising performance using simulated and experimental EM density maps of several complexes.
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Affiliation(s)
- S Jonić
- IMPMC, Sorbonne Universités - CNRS UMR 7590, UPMC Univ Paris 6, MNHN, IRD UMR 206, 75005 Paris, France.
| | - J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain
| | - R Melero
- Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain
| | - J Gómez-Blanco
- Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología - CSIC, Campus de Cantoblanco, Darwin 3, 28049 Madrid, Spain
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Vargas J, Otón J, Marabini R, Carazo JM, Sorzano COS. Particle alignment reliability in single particle electron cryomicroscopy: a general approach. Sci Rep 2016; 6:21626. [PMID: 26899789 PMCID: PMC4761946 DOI: 10.1038/srep21626] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/27/2016] [Indexed: 11/09/2022] Open
Abstract
Electron Microscopy is reaching new capabilities thanks to the combined effect of new technologies and new image processing methods. However, the reconstruction process is still complex, requiring many steps and elaborated optimization procedures. Therefore, the possibility to reach a wrong structure exists, justifying the need of robust statistical tests. In this work, we present a conceptually simple alignment test, which does not require tilt-pair images, to evaluate the alignment consistency between a set of projection images with respect to a given 3D density map. We test the approach on a number of problems in 3DEM, especially the ranking and evaluation of initial 3D volumes and high resolution 3D maps, where we show its usefulness in providing an objective evaluation for maps that have recently been subject to a strong controversy in the field. Additionally, this alignment statistical test can be linked to the early stages of structure solving of new complexes, streamlining the whole process.
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Affiliation(s)
- J Vargas
- National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Autnoma, 28049 Cantoblanco, Madrid, Spain
| | - J Otón
- National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Autnoma, 28049 Cantoblanco, Madrid, Spain
| | - R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Autnoma, 28049 Cantoblanco, Madrid, Spain
| | - C O S Sorzano
- National Center for Biotechnology (CSIC), c/Darwin, 3, Campus Universidad Autnoma, 28049 Cantoblanco, Madrid, Spain.,Bioengineering Lab. Univ. San Pablo CEU. Campus Urb. Monteprncipe s/n. 28668 Boadilla del Monte, Madrid, Spain
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Segura J, Sorzano COS, Cuenca-Alba J, Aloy P, Carazo JM. Using neighborhood cohesiveness to infer interactions between protein domains. Bioinformatics 2015; 31:2545-52. [DOI: 10.1093/bioinformatics/btv188] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/28/2015] [Indexed: 01/18/2023] Open
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35
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Abrishami V, Zaldívar-Peraza A, de la Rosa-Trevín JM, Vargas J, Otón J, Marabini R, Shkolnisky Y, Carazo JM, Sorzano COS. A pattern matching approach to the automatic selection of particles from low-contrast electron micrographs. Bioinformatics 2013; 29:2460-8. [DOI: 10.1093/bioinformatics/btt429] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Vargas J, Otón J, Marabini R, Jonic S, de la Rosa-Trevín JM, Carazo JM, Sorzano COS. FASTDEF: fast defocus and astigmatism estimation for high-throughput transmission electron microscopy. J Struct Biol 2012; 181:136-48. [PMID: 23261401 DOI: 10.1016/j.jsb.2012.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 12/07/2012] [Accepted: 12/11/2012] [Indexed: 10/27/2022]
Abstract
In this work we present a fast and automated algorithm for estimating the contrast transfer function (CTF) of a transmission electron microscope. The approach is very suitable for High Throughput work because: (a) it does not require any initial defocus estimation, (b) it is almost an order of magnitude faster than existing approaches, (c) it opens the way to well-defined extensions to the estimation of higher order aberrations, at the same time that provides defocus and astigmatism estimations comparable in accuracy to well established methods, such as Xmipp and CTFFIND3 approaches. The new algorithm is based on obtaining the wrapped modulating phase of the power spectra density pattern by the use of a quadrature filter. This phase is further unwrapped in order to obtain the continuous and smooth absolute phase map; then a Zernike polynomial fitting is performed and the defocus and astigmatism parameters are determined. While the method does not require an initial estimation of the defocus parameters or any non-linear optimization procedure, these approaches can be used if further refinement is desired. Results of the CTF estimation method are presented for standard negative stained images, cryo-electron microscopy images in the absence of carbon support, as well as micrographs with only ice. Additionally, we have also tested the proposed method with micrographs acquired from tilted and untilted samples, obtaining good results. The algorithm is freely available as a part of the Xmipp package [http://xmipp.cnb.csic.es].
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Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco, Madrid, Spain.
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Vargas J, Restrepo R, Estrada JC, Sorzano COS, Du YZ, Carazo JM. Shack-Hartmann centroid detection using the spiral phase transform. Appl Opt 2012; 51:7362-7367. [PMID: 23089793 DOI: 10.1364/ao.51.007362] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/10/2012] [Indexed: 06/01/2023]
Abstract
We present a Shack-Hartmann (SH) centroid detection algorithm capable to measure in presence of strong noise, background illumination and spot modulating signals, which are typical limiting factors of traditional centroid detection algorithms. The proposed method is based on performing a normalization of the SH pattern using the spiral phase transform method and Fourier filtering. The spot centroids are then obtained using global thresholding and weighted average methods. We have tested the algorithm with simulations and experimental data obtaining satisfactory results. A complete MATLAB package that can reproduce all the results can be downloaded from [http://goo.gl/o2JhD].
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Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
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Vargas J, Quiroga JA, Sorzano COS, Estrada JC, Carazo JM. Two-step demodulation based on the Gram-Schmidt orthonormalization method. Opt Lett 2012; 37:443-5. [PMID: 22297380 DOI: 10.1364/ol.37.000443] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This Letter presents an efficient, fast, and straightforward two-step demodulating method based on a Gram-Schmidt (GS) orthonormalization approach. The phase-shift value has not to be known and can take any value inside the range (0,2π), excluding the singular case, where it corresponds to π. The proposed method is based on determining an orthonormalized interferogram basis from the two supplied interferograms using the GS method. We have applied the proposed method to simulated and experimental interferograms, obtaining satisfactory results. A complete MATLAB software package is provided at http://goo.gl/IZKF3.
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Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, Cantoblanco (Madrid), Spain.
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Abstract
A two-step phase-shifting method, that can demodulate open- and closed-fringed patterns without local sign ambiguity is presented. The proposed method only requires a constant phase-shift between the two interferograms. This phase-shift does not need to be known and can take any value inside the range (0, 2π), excluding the singular case where it corresponds to π. The proposed method is based on determining first the fringe direction map by a regularized optical flow algorithm. After that, we apply the spiral phase transform (SPT) to one of the fringe patterns and we determine its quadrature signal using the previously determined direction. The proposed technique has been applied to simulated and experimental interferograms obtaining satisfactory results. A complete MATLAB software package is provided in [http://goo.gl/Snnz7].
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Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
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Arganda-Carreras I, Sorzano COS, Thévenaz P, Muñoz-Barrutia A, Kybic J, Marabini R, Carazo JM, Ortiz-de Solorzano C. Non-rigid consistent registration of 2D image sequences. Phys Med Biol 2010; 55:6215-42. [DOI: 10.1088/0031-9155/55/20/012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Sorzano COS, Recarte E, Alcorlo M, Bilbao-Castro JR, San-Martín C, Marabini R, Carazo JM. Automatic particle selection from electron micrographs using machine learning techniques. J Struct Biol 2009; 167:252-60. [PMID: 19555764 DOI: 10.1016/j.jsb.2009.06.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 10/20/2022]
Abstract
The 3D reconstruction of biological specimens using Electron Microscopy is currently capable of achieving subnanometer resolution. Unfortunately, this goal requires gathering tens of thousands of projection images that are frequently selected manually from micrographs. In this paper we introduce a new automatic particle selection that learns from the user which particles are of interest. The training phase is semi-supervised so that the user can correct the algorithm during picking and specifically identify incorrectly picked particles. By treating such errors specially, the algorithm attempts to minimize the number of false positives. We show that our algorithm is able to produce datasets with fewer wrongly selected particles than previously reported methods. Another advantage is that we avoid the need for an initial reference volume from which to generate picking projections by instead learning which particles to pick from the user. This package has been made publicly available in the open-source package Xmipp.
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Affiliation(s)
- C O S Sorzano
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain.
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Sorzano COS, Messaoudi C, Eibauer M, Bilbao-Castro JR, Hegerl R, Nickell S, Marco S, Carazo JM. Marker-free image registration of electron tomography tilt-series. BMC Bioinformatics 2009; 10:124. [PMID: 19397789 PMCID: PMC2694187 DOI: 10.1186/1471-2105-10-124] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 04/27/2009] [Indexed: 12/03/2022] Open
Abstract
Background Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal. Results In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography. Conclusion Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.
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Iriarte A, Sorzano COS, Carazo JM, Rubio JL, Marabini R. A theoretical model for EM-ML reconstruction algorithms applied to rotating PET scanners. Phys Med Biol 2009; 54:1909-34. [PMID: 19265206 DOI: 10.1088/0031-9155/54/7/004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this paper we show how to compute the normalizing and the system matrix terms of the EM-ML reconstruction algorithm for rotating planar detector PET scanners. The method introduced is valid for either pixelated or continuous scintillators. We base our computations in geometrical considerations, but other effects of the PET process can be easily included. In this regard, the intrinsic resolution of the detection system, the depth of interaction (DOI) of the incident gamma rays and the efficiency of the scintillators have been modeled in our development. The computation of the normalizing term and the system matrix is valid for any basis function used for the discrete approximation of the radionuclide concentration. We show that our computations are comparable to those of a Monte Carlo method at a small fraction of the computational cost.
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Affiliation(s)
- A Iriarte
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Bilbao-Castro JR, Marabini R, Sorzano COS, García I, Carazo JM, Fernández JJ. Exploiting desktop supercomputing for three-dimensional electron microscopy reconstructions using ART with blobs. J Struct Biol 2008; 165:19-26. [PMID: 18940260 DOI: 10.1016/j.jsb.2008.09.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 10/21/2022]
Abstract
Three-dimensional electron microscopy allows direct visualization of biological macromolecules close to their native state. The high impact of this technique in the structural biology field is highly correlated with the development of new image processing algorithms. In order to achieve subnanometer resolution, the size and number of images involved in a three-dimensional reconstruction increase and so do computer requirements. New chips integrating multiple processors are hitting the market at a reduced cost. This high-integration, low-cost trend has just begun and is expected to bring real supercomputers to our laboratory desktops in the coming years. This paper proposes a parallel implementation of a computation-intensive algorithm for three-dimensional reconstruction, ART, that takes advantage of the computational power in modern multicore platforms. ART is a sophisticated iterative reconstruction algorithm that has turned out to be well suited for the conditions found in three-dimensional electron microscopy. In view of the performance obtained in this work, these modern platforms are expected to play an important role to face the future challenges in three-dimensional electron microscopy.
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Affiliation(s)
- J R Bilbao-Castro
- Dept. Arquitectura de Computadores y Electrónica, Universidad de Almería, 04120 Almería, Spain.
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Sorzano COS, Jonic S, Núñez-Ramírez R, Boisset N, Carazo JM. Fast, robust, and accurate determination of transmission electron microscopy contrast transfer function. J Struct Biol 2007; 160:249-62. [PMID: 17911028 DOI: 10.1016/j.jsb.2007.08.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 08/18/2007] [Accepted: 08/22/2007] [Indexed: 01/24/2023]
Abstract
Transmission electron microscopy, as most imaging devices, introduces optical aberrations that in the case of thin specimens are usually modeled in Fourier space by the so-called contrast transfer function (CTF). Accurate determination of the CTF is crucial for its posterior correction. Furthermore, the CTF estimation must be fast and robust if high-throughput three-dimensional electron microscopy (3DEM) studies are to be carried out. In this paper we present a robust algorithm that fits a theoretical CTF model to the power spectrum density (PSD) measured on a specific micrograph or micrograph area. Our algorithm is capable of estimating the envelope of the CTF which is absolutely needed for the correction of the CTF amplitude changes.
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Affiliation(s)
- C O S Sorzano
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain.
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Macías JR, Jiménez-Lozano N, Carazo JM. Integrating electron microscopy information into existing Distributed Annotation Systems. J Struct Biol 2007; 158:205-13. [PMID: 17400476 DOI: 10.1016/j.jsb.2007.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Revised: 12/19/2006] [Accepted: 02/13/2007] [Indexed: 10/23/2022]
Abstract
The increase of daily released bioinformatic data has generated new ways of organising and disseminating information. Specifically, in the field of sequence data, many efforts have been made not only to store information in databases, but also to annotate it and then share these annotations through a standard XML (eXtensible Markup Language) protocol and appropriate integration clients. This is the context in which the Distributed Annotation System (DAS) has emerged in genomics. Additionally, initiatives in the field of structural data, such as the extension of DAS to atomic resolution data, which generated the SPICE client, have also occurred. This paper presents 3D-EM DAS, a further extension of the DAS protocol that allows sharing annotations about hybrid models. This annotation system has been built on the basis of the EMDB, which stores Three-dimensional Electron Microscopy (3D-EM) volumes, PDB, which houses atomic coordinates, and UniProt (for protein sequences) databases. In this way, annotations for sequences, atomic coordinates, and 3D-EM volumes are collected and displayed through a single graphical visualization client. Thus, users have an integrated view of all the annotations together with the whole macromolecule (3D-EM map coming from EMDB), the atomic resolution structures fitted into it (coordinates coming from PDB) and the sequences corresponding to each of the structures (from UniProt).
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Affiliation(s)
- J R Macías
- Unidad de Biocomputación, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco UAM, c/ Darwin 3, 28049 Madrid, Spain.
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Pascual-Montano A, Carazo JM, Kochi K, Lehmann D, Pascual-Marqui RD. Nonsmooth nonnegative matrix factorization (nsNMF). IEEE Trans Pattern Anal Mach Intell 2006; 28:403-15. [PMID: 16526426 DOI: 10.1109/tpami.2006.60] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
We propose a novel nonnegative matrix factorization model that aims at finding localized, part-based, representations of nonnegative multivariate data items. Unlike the classical nonnegative matrix factorization (NMF) technique, this new model, denoted "nonsmooth nonnegative matrix factorization" (nsNMF), corresponds to the optimization of an unambiguous cost function designed to explicitly represent sparseness, in the form of nonsmoothness, which is controlled by a single parameter. In general, this method produces a set of basis and encoding vectors that are not only capable of representing the original data, but they also extract highly localized patterns, which generally lend themselves to improved interpretability. The properties of this new method are illustrated with several data sets. Comparisons to previously published methods show that the new nsNMF method has some advantages in keeping faithfulness to the data in the achieving a high degree of sparseness for both the estimated basis and the encoding vectors and in better interpretability of the factors.
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Affiliation(s)
- Alberto Pascual-Montano
- Computer Architecture and System Engineering Department, Facultad de Ciencias Físicas, Universidad Complutense, Madrid, Spain.
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Sorzano COS, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SHW, Carazo JM, Pascual-Montano A. XMIPP: a new generation of an open-source image processing package for electron microscopy. J Struct Biol 2005; 148:194-204. [PMID: 15477099 DOI: 10.1016/j.jsb.2004.06.006] [Citation(s) in RCA: 353] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 06/04/2004] [Indexed: 11/30/2022]
Abstract
X-windows based microscopy image processing package (Xmipp) is a specialized suit of image processing programs, primarily aimed at obtaining the 3D reconstruction of biological specimens from large sets of projection images acquired by transmission electron microscopy. This public-domain software package was introduced to the electron microscopy field eight years ago, and since then it has changed drastically. New methodologies for the analysis of single-particle projection images have been added to classification, contrast transfer function correction, angular assignment, 3D reconstruction, reconstruction of crystals, etc. In addition, the package has been extended with functionalities for 2D crystal and electron tomography data. Furthermore, its current implementation in C++, with a highly modular design of well-documented data structures and functions, offers a convenient environment for the development of novel algorithms. In this paper, we present a general overview of a new generation of Xmipp that has been re-engineered to maximize flexibility and modularity, potentially facilitating its integration in future standardization efforts in the field. Moreover, by focusing on those developments that distinguish Xmipp from other packages available, we illustrate its added value to the electron microscopy community.
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Affiliation(s)
- C O S Sorzano
- Unidad de Biocomputación, Centro Nacional de Biotecnología (CSIC), Campus Universidad Autónoma s/n, 28049 Cantoblanco, Madrid, Spain.
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Sorzano COS, Jonić S, El-Bez C, Carazo JM, De Carlo S, Thévenaz P, Unser M. A multiresolution approach to orientation assignment in 3D electron microscopy of single particles. J Struct Biol 2005; 146:381-92. [PMID: 15099579 DOI: 10.1016/j.jsb.2004.01.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Revised: 01/13/2004] [Indexed: 11/26/2022]
Abstract
Three-dimensional (3D) electron microscopy (3DEM) aims at the determination of the spatial distribution of the Coulomb potential of macromolecular complexes. The 3D reconstruction of a macromolecule using single-particle techniques involves thousands of 2D projections. One of the key parameters required to perform such a 3D reconstruction is the orientation of each projection image as well as its in-plane orientation. This information is unknown experimentally and must be determined using image-processing techniques. We propose the use of wavelets to match the experimental projections with those obtained from a reference 3D model. The wavelet decomposition of the projection images provides a framework for a multiscale matching algorithm in which speed and robustness to noise are gained. Furthermore, this multiresolution approach is combined with a novel orientation selection strategy. Results obtained from computer simulations as well as experimental data encourage the use of this approach.
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Affiliation(s)
- C O S Sorzano
- Escuela Politécnica Superior, Universidad San Pablo-CEU, Campus Urb., Madrid, Spain.
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Sorzano COS, de la Fraga LG, Clackdoyle R, Carazo JM. Normalizing projection images: a study of image normalizing procedures for single particle three-dimensional electron microscopy. Ultramicroscopy 2004; 101:129-38. [PMID: 15450658 DOI: 10.1016/j.ultramic.2004.04.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Revised: 04/08/2004] [Accepted: 04/13/2004] [Indexed: 10/26/2022]
Abstract
In the process of three-dimensional reconstruction of single particle biological macromolecules several hundreds, or thousands, of projection images are taken from tens or hundreds of independently digitized micrographs. These different micrographs show differences in the background grey level and particle contrast and, therefore, have to be normalized by scaling their pixel values before entering the reconstruction process. In this work several normalization procedures are studied using a statistical comparison framework. We finally show that the use of the different normalization methods affects the reconstruction quality, providing guidance on the choice of normalization procedures.
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Affiliation(s)
- C O S Sorzano
- Biocomputing Unit, National Center of Biotechnology (CSIC), Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
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