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Integration of Cryo-EM Model Building Software in Scipion

  • M. Martínez
    M. Martínez
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by M. Martínez
  • A. Jiménez-Moreno
    A. Jiménez-Moreno
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • D. Maluenda
    D. Maluenda
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by D. Maluenda
  • E. Ramírez-Aportela
    E. Ramírez-Aportela
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • R. Melero
    R. Melero
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by R. Melero
  • A. Cuervo
    A. Cuervo
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by A. Cuervo
  • P. Conesa
    P. Conesa
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
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  • L. del Caño
    L. del Caño
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by L. del Caño
  • Y. C. Fonseca
    Y. C. Fonseca
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • R. Sánchez-García
    R. Sánchez-García
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • D. Strelak
    D. Strelak
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    Institute of Computer Science, Masaryk University, Botanická 68a, 60200 Brno, Czech Republic
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  • J. J. Conesa
    J. J. Conesa
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by J. J. Conesa
  • E. Fernández-Giménez
    E. Fernández-Giménez
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • F. de Isidro
    F. de Isidro
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by F. de Isidro
  • C. O. S. Sorzano
    C. O. S. Sorzano
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
  • J. M. Carazo
    J. M. Carazo
    CNB-CSIC, C/Darwin 3, 28049 Madrid, Spain
    More by J. M. Carazo
  • , and 
  • R. Marabini*
    R. Marabini
    Escuela Politécnica, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente 11, 28049 Madrid, Spain
    *E-mail: [email protected]
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Cite this: J. Chem. Inf. Model. 2020, 60, 5, 2533–2540
Publication Date (Web):January 29, 2020
https://doi.org/10.1021/acs.jcim.9b01032
Copyright © 2020 American Chemical Society

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    Abstract

    Abstract Image

    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.

    Cited By

    This article is cited by 16 publications.

    1. Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro. Faces of Contemporary CryoEM Information and Modeling. Journal of Chemical Information and Modeling 2020, 60 (5) , 2407-2409. https://doi.org/10.1021/acs.jcim.0c00481
    2. Tami Khazma, Atira Grossman, Julia Guez-Haddad, Chengye Feng, Hadas Dabas, Radhika Sain, Michal Weitman, Ran Zalk, Michail N. Isupov, Marc Hammarlund, Michael Hons, Yarden Opatowsky. Structure-function analysis of ceTIR-1/hSARM1 explains the lack of Wallerian axonal degeneration in C. elegans. Cell Reports 2023, 42 (9) , 113026. https://doi.org/10.1016/j.celrep.2023.113026
    3. Miki Nakano, Osamu Miyashita, Florence Tama. Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction. Structural Dynamics 2023, 10 (2) https://doi.org/10.1063/4.0000175
    4. Tami Khazma, Yarden Golan-Vaishenker, Julia Guez-Haddad, Atira Grossman, Radhika Sain, Michal Weitman, Alexander Plotnikov, Ran Zalk, Avraham Yaron, Michael Hons, Yarden Opatowsky. A duplex structure of SARM1 octamers stabilized by a new inhibitor. Cellular and Molecular Life Sciences 2023, 80 (1) https://doi.org/10.1007/s00018-022-04641-3
    5. Daniel X. Du, Anthony W.P. Fitzpatrick. Design of an ultrafast pulsed ponderomotive phase plate for cryo-electron tomography. Cell Reports Methods 2023, 3 (1) , 100387. https://doi.org/10.1016/j.crmeth.2022.100387
    6. Pablo Conesa, Yunior C. Fonseca, Jorge Jiménez de la Morena, Grigory Sharov, Jose Miguel de la Rosa-Trevín, Ana Cuervo, Alberto García Mena, Borja Rodríguez de Francisco, Daniel del Hoyo, David Herreros, Daniel Marchan, David Strelak, Estrella Fernández-Giménez, Erney Ramírez-Aportela, Federico Pedro de Isidro-Gómez, Irene Sánchez, James Krieger, José Luis Vilas, Laura del Cano, Marcos Gragera, Mikel Iceta, Marta Martínez, Patricia Losana, Roberto Melero, Roberto Marabini, José María Carazo, Carlos Oscar Sánchez Sorzano. Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology. Biological Imaging 2023, 3 https://doi.org/10.1017/S2633903X23000132
    7. J. Jiménez de la Morena, P. Conesa, Y.C. Fonseca, F.P. de Isidro-Gómez, D. Herreros, E. Fernández-Giménez, D. Strelak, E. Moebel, T.O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J.J. Conesa, A. Cuervo, P. Losana, I. Sánchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castaño-Díez, A. Koster, J.G. Piccirillo, J.L. Vilas, J. Otón, R. Marabini, C.O.S. Sorzano, J.M. Carazo. ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. Journal of Structural Biology 2022, 214 (3) , 107872. https://doi.org/10.1016/j.jsb.2022.107872
    8. Anastassia L. Kantsadi, Georgios N. Hatzopoulos, Pierre Gönczy, Ioannis Vakonakis. Structures of SAS-6 coiled coil hold implications for the polarity of the centriolar cartwheel. Structure 2022, 30 (5) , 671-684.e5. https://doi.org/10.1016/j.str.2022.02.005
    9. Georgios N. Hatzopoulos, Tim Kükenshöner, Niccolò Banterle, Tatiana Favez, Isabelle Flückiger, Virginie Hamel, Santiago Andany, Georg E. Fantner, Oliver Hantschel, Pierre Gönczy. Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly. Nature Communications 2021, 12 (1) https://doi.org/10.1038/s41467-021-23897-0
    10. David Strelak, Amaya Jiménez-Moreno, José L. Vilas, Erney Ramírez-Aportela, Ruben Sánchez-García, David Maluenda, Javier Vargas, David Herreros, Estrella Fernández-Giménez, Federico P. de Isidro-Gómez, Jan Horacek, David Myska, Martin Horacek, Pablo Conesa, Yunior C. Fonseca-Reyna, Jorge Jiménez, Marta Martínez, Mohamad Harastani, Slavica Jonić, Jiri Filipovic, Roberto Marabini, José M. Carazo, Carlos O. S. Sorzano. Advances in Xmipp for Cryo–Electron Microscopy: From Xmipp to Scipion. Molecules 2021, 26 (20) , 6224. https://doi.org/10.3390/molecules26206224
    11. Jorge Jiménez, Federico De Isidro, Estrella Fernández Jiménez, David Herreros Calero, Yunior Fonseca, Pablo Conesa, Ana Cuervo, Javier Conesa, Roberto Melero, Jose Maria Carazo, Carlos Oscar Sorzano. Electron Tomography Workflows using Scipion. Microscopy and Microanalysis 2021, 27 (S1) , 2578-2579. https://doi.org/10.1017/S1431927621009156
    12. Roberto Marabini, Gabriela N. Condezo, Mart Krupovic, Rosa Menéndez-Conejero, Josué Gómez-Blanco, Carmen San Martín. Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins. Science Advances 2021, 7 (14) https://doi.org/10.1126/sciadv.abe6008
    13. Marta Pérez-Illana, Marta Martínez, Gabriela N. Condezo, Mercedes Hernando-Pérez, Casandra Mangroo, Martha Brown, Roberto Marabini, Carmen San Martín. Cryo-EM structure of enteric adenovirus HAdV-F41 highlights structural variations among human adenoviruses. Science Advances 2021, 7 (9) https://doi.org/10.1126/sciadv.abd9421
    14. Carlos Oscar S. Sorzano, Amaya Jiménez-Moreno, David Maluenda, Erney Ramírez-Aportela, Marta Martínez, Ana Cuervo, Robert Melero, Jose Javier Conesa, Ruben Sánchez-García, David Strelak, Jiri Filipovic, Estrella Fernández-Giménez, Federico de Isidro-Gómez, David Herreros, Pablo Conesa, Laura del Caño, Yunior Fonseca, Jorge Jiménez de la Morena, Jose Ramon Macías, Patricia Losana, Roberto Marabini, Jose-Maria Carazo. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. 2021, 257-289. https://doi.org/10.1007/978-1-0716-1406-8_13
    15. Michael Sporny, Julia Guez-Haddad, Tami Khazma, Avraham Yaron, Moshe Dessau, Yoel Shkolnisky, Carsten Mim, Michail N Isupov, Ran Zalk, Michael Hons, Yarden Opatowsky. Structural basis for SARM1 inhibition and activation under energetic stress. eLife 2020, 9 https://doi.org/10.7554/eLife.62021
    16. Roberto Melero, Carlos Oscar S. Sorzano, Brent Foster, José-Luis Vilas, Marta Martínez, Roberto Marabini, Erney Ramírez-Aportela, Ruben Sanchez-Garcia, David Herreros, Laura del Caño, Patricia Losana, Yunior C. Fonseca-Reyna, Pablo Conesa, Daniel Wrapp, Pablo Chacon, Jason S. McLellan, Hemant D. Tagare, Jose-Maria Carazo. Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. IUCrJ 2020, 7 (6) , 1059-1069. https://doi.org/10.1107/S2052252520012725

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