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

被引：14

作者：

Conesa Mingo, Pablo ^{[1
]}

Gutierrez, Jose ^{[1
]}

Quintana, Adrian ^{[1
]}

de la Rosa Trevin, Jose Miguel ^{[1
]}

Zaldivar-Peraza, Airen ^{[1
]}

Cuenca Alba, Jesus ^{[1
]}

Kazemi, Mohsen ^{[1
]}

Vargas, Javier ^{[1
]}

del Cano, Laura ^{[1
]}

Segura, Joan ^{[1
]}

Sorzano, Carlos Oscar S. ^{[1
]}

Maria Carazo, Jose ^{[1
]}

机构：

[1] Ctr Nacl Biotecnol CNB CSIC, Madrid 28049, Spain

来源：

PROTEIN SCIENCE | 2018年 / 27卷 / 01期

基金：

欧盟地平线“2020”;

关键词：

cryo-electron microscopy; web tools; validation; visualization; workflow; ELECTRON; RESOLUTION; SUITE;

D O I：

10.1002/pro.3315

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process.

引用

页码：269 / 275

页数：7

共 21 条

[1] Alignment of direct detection device micrographs using a robust Optical Flow approach [J].

Abrishami, Vahid ;

Vargas, Javier ;

Li, Xueming ;

Cheng, Yifan ;

Marabini, Roberto ;

Sanchez Sorzano, Carlos Oscar ;

Maria Carazo, Jose .

JOURNAL OF STRUCTURAL BIOLOGY, 2015, 189 (03) :163-176

[2] One number does not fit all: Mapping local variations in resolution in cryo-EM reconstructions [J].

Cardone, Giovanni ;

Heymann, J. Bernard ;

Steven, Alasdair C. .

JOURNAL OF STRUCTURAL BIOLOGY, 2013, 184 (02) :226-236

[3]

Cuenca-Alba J, 2017, J STRUCT BIOL, P1047

[4] Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy [J].

de la Rosa-Trevin, J. M. ;

Quintana, A. ;

del Cano, L. ;

Zaldivar, A. ;

Foche, I. ;

Gutierrez, J. ;

Gomez-Blanco, J. ;

Burguet-Castell, J. ;

Cuenca-Alba, J. ;

Abrishami, V. ;

Vargas, J. ;

Oton, J. ;

Sharov, G. ;

Vilas, J. L. ;

Navas, J. ;

Conesa, P. ;

Kazemi, M. ;

Marabini, R. ;

Sorzano, C. O. S. ;

Carazo, J. M. .

JOURNAL OF STRUCTURAL BIOLOGY, 2016, 195 (01) :93-99

[5] The EGI Federated Cloud e-Infrastructure [J].

Fernandez-del-Castillo, Enol ;

Scardaci, Diego ;

Lopez Garcia, Alvaro .

1ST INTERNATIONAL CONFERENCE ON CLOUD FORWARD: FROM DISTRIBUTED TO COMPLETE COMPUTING, 2015, 68 :196-205

[6]

Heymann J. B., 2014, MICROSC MICROANAL, V20, P792

[7]

Kucukelbir A, 2014, NAT METHODS, V11, P63, DOI [10.1038/nmeth.2727, 10.1038/NMETH.2727]

[8]

Mosca R, 2013, NUCLEIC ACIDS RES, V42, P374

[9] NGL Viewer: a web application for molecular visualization [J].

Rose, Alexander S. ;

Hildebrand, Peter W. .

NUCLEIC ACIDS RESEARCH, 2015, 43 (W1) :W576-W579

[10] Validating maps from single particle electron cryomicroscopy [J].

Rosenthal, Peter B. ;

Rubinstein, John L. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2015, 34 :135-144

← 1 2 3 →