Integration of Cryo-EM Model Building Software in Scipion

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1. Shuya Kate Huang, John L. Rubinstein, Lewis E. Kay. Cryo-EM of the Nucleosome Core Particle Bound to Ran-RCC1 Reveals a Dynamic Complex. Biochemistry 2024, 63 (7) , 880-892. https://doi.org/10.1021/acs.biochem.3c00724
2. Daniel Del Hoyo, Martin Salinas, Alba Lomas, Eugenia Ulzurrun, Nuria E. Campillo, Carlos Oscar Sorzano. Scipion-Chem: An Open Platform for Virtual Drug Screening. Journal of Chemical Information and Modeling 2023, 63 (24) , 7873-7885. https://doi.org/10.1021/acs.jcim.3c01085
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6. 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
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8. 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
9. 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
10. 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
11. 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
12. 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
13. 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
14. 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
15. 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
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17. 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
18. 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