Scipion web tools: Easy to use cryo-EM image processing over the web

Protein Science

Volumn 27, Issue 1, 2018, Pages 269-275

  Conesa Mingo, Pablo ^a   Gutierrez, José ^a   Quintana, Adrián ^a   de la Rosa Trevín, José Miguel ^a   Zaldívar Peraza, Airén ^a   Cuenca Alba, Jesús ^a   Kazemi, Mohsen ^a   Vargas, Javier ^a   del Cano, Laura ^a   Segura, Joan ^a   Sorzano, Carlos Oscar S ^a   Carazo, Jose María ^a  

^a CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

cryo electron microscopy; validation; visualization; web tools; workflow

Indexed keywords

ALGORITHM; ARTICLE; CLOUD COMPUTING; CRYOELECTRON MICROSCOPY; DATA BASE; IMAGE ANALYSIS; IMAGE PROCESSING; MACROMOLECULE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; RELIABILITY; WEB BROWSER; WORKFLOW; INTERNET; SOFTWARE;

CRYOELECTRON MICROSCOPY; IMAGE PROCESSING, COMPUTER-ASSISTED; INTERNET; SOFTWARE;

EID: 85032900189     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.3315     Document Type: Article

References (21)

1. Vinothkumar KR, Henderson R (2016) Single particle electron microscopy: trends, issue and future perspective. Q Rev Biophys 49:e13.
2. Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, Evans PR, Keegan RM, Krissinel EB, Leslie AGW, McCoy A, McNicholas SJ, Murshudov GN, Pannu NS, Potterton EA, Powell HR, Read RJ, Vagin A, Wilson KS (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D 67:235–242.
3. TA, Wassenaar M, van Dijk N, Loureiro-Ferreira G, van der Schot SJ, de Vries C, Schmitz J, van der Zwan R, Boelens A, Giachetti L, Ferella A, Rosato I, Bertini T, Herrmann HRA, Jonker A, Bagaria V, Jaravine P, Güntert H, Schwalbe WF, Vranken JF, Doreleijers G, Vriend GW, Vuister D, Franke A, Kikhney DI, Svergun RH, Fogh J, Ionides ED, Laue C, Spronk S, Jurkša M, Verlato S, Badoer S, Dal Pra M, Mazzucato E, Frizziero Alexandre MJJ Bonvin (Dec 2012) Wenmr: Structural biology on the grid. J Grid Comput 10:743–767.
4. Yoshioka C, Lyumkis D, Carragher B, Potter CS (2013) Maskiton: Interactive, web-based classification of single-particle electron microscopy images. J Struct Biol 182:156–163.
5. de la Rosa-Trevín JM, Quintana A, del Cano L, Zaldívar A, Foche I, Gutiérrez J, Gómez-Blanco J, Burguet-Castell J, Cuenca-Alba J, Abrishami V, Vargas J, Otón J, Sharov G, Vilas JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano COS, Carazo JM (2016) Scipion: A software framework toward integration, reproducibility and validation in 3d electron microscopy. J Struct Biol 195:93–99.
6. Rose AS, Hildebrand PW (2015) NGL Viewer: a web application for molecular visualization. Nucl. Acids Res 43:576–579.
7. Cuenca-Alba J, del Cano L, Gómez Blanco J, de la Rosa Trevín JM, Conesa P, Marabini R, Sorzano COS, Carazo JM (2017) Scipioncloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds. J Struct Biol 1047–8477.
8. Segura J, Sanchez-Garcia R, Tabas-Madrid D, Cuenca-Alba J, Sorzano COS, Carazo JM (2016) 3DIANA: 3D domain interaction analysis: A toolbox for quaternary structure modeling. Biophys J 110:766–755.
9. Abrishami V, Vargas J, Li X, Cheng Y, Marabini R, Sorzano CÓS, Carazo JM (2015) Alignment of direct detection device micrographs using a robust optical flow approach. J Struct Biol 189:163–176.
10. Tang G, Peng L, Baldwin PR, Mann DS, Jiang W, Rees I, Ludtke SJ (2007) Eman2: An extensible image processing suite for electron microscopy. J Struct Biol 157:38–46.
11. Vargas J, Alvarez-Cabrera A-L, Marabini R, Carazo JM, Sorzano COS (2014) Efficient initial volume determination from electron microscopy images of single particles. Bioinformatics 30:2891–2898.
12. Sorzano C, Vargas J, Rosa-Trevín JM, Otón J, Álvarez Cabrera A, Abrishami V, Sesmero E, Marabini R, Carazo J (2015) A statistical approach to the initial volume problem in single particle analysis by electron microscopy. J Struct Biol 189:213–219.
13. Sorzano C, Vargas J, Otón J, Abrishami V, Rosa-Trevín JM, Gómez-Blanco J, Vilas JL, Marabini R, Carazo J (2017) A review of resolution measures and related aspects in 3d electron microscopy. Progr Biophys Mol Biol 124:1–30.
14. Kucukelbir A, Sigworth FJ, Tagare HD (2014) Quantifying the local resolution of cryo-em density maps. Nat Methods 11:63–65.
15. Cardone G, Heymann JB, Steven AC (2013) One number does not fit all: Mapping local variations in resolution in cryo-em reconstructions. J Struct Biol 184:226–236.
16. Rosenthal PB, Rubinstein JL (2015) Validating maps from single particle electron cryomicroscopy. Curr Opin Struct Biol 34:135–144.
17. Heymann JB (2014) The Phantom in the Noise and Validation of 3D EM Reconstructions. Microsc Microanal 20:792–793.
18. Vargas J, Otón J, Marabini R, Carazo JM, Sorzano COS (2016) Particle alignment reliability in single particle electron cryomicroscopy: a general approach. Sci Rep 6.
19. Segura J, Sorzano COS, Cuenca-Alba J, Aloy P, Carazo JM (2015) Using neighborhood cohesiveness to infer interactions between protein domains. Bioinformatics 31:2545–2552.
20. Mosca R, Céol A, Stein A, Olivella R, Aloy P (2013) 3did: a catalog of domain-based interactions of known three-dimensional structure. Nucl Acids Res 42:374–379.
21. Fernández-del Castillo E, Scardaci D, Lopez García A (2015) The egi federated cloud e-infrastructure. Procedia Comput Sci 68:196–205.