59. Hoang TV, Cavin X, Schultz P, Ritchie DW (2013) gEMpicker: a highly parallel
GPU-accelerated particle picking tool for cryo-electron microscopy. BMC Struct Biol 13:25
60. Chen JZ, Grigorieff N (2007) SIGNATURE: a single-particle selection system for molecular
electron microscopy. J Struct Biol 157:168–173
61. Henderson R (2013) Avoiding the pitfalls of single particle cryo-electron microscopy:
Einstein from noise. Proc Nat Acad Sci USA 110:18037–18041
62. De Rosier DJ, Klug A (1968) Reconstruction of three dimensional structures from electron
micrographs. Nature 217:130–134
63. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and
WEB: processing and visualization of images in 3D electron microscopy and related fields.
J Struct Biol 116:190–199
64. Zivanov J, Nakane T, Scheres S (2018) A Bayesian approach to beam-induced motion
correction in cryo-EM single-particle analysis, bioRxiv
65. Lyumkis D, Brilot AF, Theobald DL, Grigorieff N (2013) Likelihood-based classification of
cryo-EM images using FREALIGN. J Struct Biol 183:377–388
66. de la Rosa-Trevin JM, 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 JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM
(2016) Scipion: a software framework toward integration, reproducibility and validation in
3D electron microscopy. J Struct Biol 195:93–99
67. Frank J, Shimkin B, Dowse H (1981) Spider—a modular software system for electron image
processing. Ultramicroscopy 6:343–357
68. van Heel M, Frank J (1981) Use of multivariate statistics in analysing the images of
biological macromolecules. Ultramicroscopy 6:187–194
69. Scheres SH (2012) A Bayesian view on cryo-EM structure determination. J Mol Biol
415:406–418
70. Van Heel M (1987) Angular reconstitution: a posteriori assignment of projection directions
for 3D reconstruction. Ultramicroscopy 21:111–123
71. Penczek PA, Grassucci RA, Frank J (1994) The ribosome at improved resolution: new
techniques for merging and orientation refinement in 3D cryo-electron microscopy of
biological particles. Ultramicroscopy 53:251–270
72. Radermacher M, Wagenknecht T, Verschoor A, Frank J (1987) Three-dimensional
reconstruction from a single-exposure, random conical tilt series applied to the 50S
ribosomal subunit of Escherichia coli. J Microsc 146:113–136
73. Penczek PA (2014).http://sparx-em.org/sparxwiki/sxviper
74. Natesh R, Clare DK, Farr GW, Horwich AL, Saibil HR (2018) A two-domain folding
intermediate of RuBisCO in complex with the GroEL chaperonin. Int J Biol Macromol
118:671–675
75. Bartesaghi A, Aguerrebere C, Falconieri V, Banerjee S, Earl LA, Zhu X, Grigorieff N,
Milne JLS, Sapiro G, Wu X, Subramaniam S (2018) Atomic resolution cryo-EM structure of
beta-galactosidase. Structure 26(848–856):e3
76. Penczek PA (2010) Resolution measures in molecular electron microscopy. Methods
Enzymol 482:73–100
77. Harauz G, van Heel M (1986) Exact filters for general geometry three-dimensional
reconstruction. Optik 73:146–156
78. van Heel M, Schatz M (2005) Fourier shell correlation threshold criteria. J Struct Biol
151:250–262
79. Rosenthal PB, Henderson R (2003) Optimal determination of particle orientation, absolute
hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333:721–745
80. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z,
Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB,
Rossmann MG, Schmid MF, Schroder GF, Steven AC, Stokes DL, Westbrook JD,
Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL (2012)
Outcome of the first electron microscopy validation task force meeting. Structure 20:205–214
398
R. Natesh
GPU-accelerated particle picking tool for cryo-electron microscopy. BMC Struct Biol 13:25
60. Chen JZ, Grigorieff N (2007) SIGNATURE: a single-particle selection system for molecular
electron microscopy. J Struct Biol 157:168–173
61. Henderson R (2013) Avoiding the pitfalls of single particle cryo-electron microscopy:
Einstein from noise. Proc Nat Acad Sci USA 110:18037–18041
62. De Rosier DJ, Klug A (1968) Reconstruction of three dimensional structures from electron
micrographs. Nature 217:130–134
63. Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A (1996) SPIDER and
WEB: processing and visualization of images in 3D electron microscopy and related fields.
J Struct Biol 116:190–199
64. Zivanov J, Nakane T, Scheres S (2018) A Bayesian approach to beam-induced motion
correction in cryo-EM single-particle analysis, bioRxiv
65. Lyumkis D, Brilot AF, Theobald DL, Grigorieff N (2013) Likelihood-based classification of
cryo-EM images using FREALIGN. J Struct Biol 183:377–388
66. de la Rosa-Trevin JM, 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 JL, Navas J, Conesa P, Kazemi M, Marabini R, Sorzano CO, Carazo JM
(2016) Scipion: a software framework toward integration, reproducibility and validation in
3D electron microscopy. J Struct Biol 195:93–99
67. Frank J, Shimkin B, Dowse H (1981) Spider—a modular software system for electron image
processing. Ultramicroscopy 6:343–357
68. van Heel M, Frank J (1981) Use of multivariate statistics in analysing the images of
biological macromolecules. Ultramicroscopy 6:187–194
69. Scheres SH (2012) A Bayesian view on cryo-EM structure determination. J Mol Biol
415:406–418
70. Van Heel M (1987) Angular reconstitution: a posteriori assignment of projection directions
for 3D reconstruction. Ultramicroscopy 21:111–123
71. Penczek PA, Grassucci RA, Frank J (1994) The ribosome at improved resolution: new
techniques for merging and orientation refinement in 3D cryo-electron microscopy of
biological particles. Ultramicroscopy 53:251–270
72. Radermacher M, Wagenknecht T, Verschoor A, Frank J (1987) Three-dimensional
reconstruction from a single-exposure, random conical tilt series applied to the 50S
ribosomal subunit of Escherichia coli. J Microsc 146:113–136
73. Penczek PA (2014).http://sparx-em.org/sparxwiki/sxviper
74. Natesh R, Clare DK, Farr GW, Horwich AL, Saibil HR (2018) A two-domain folding
intermediate of RuBisCO in complex with the GroEL chaperonin. Int J Biol Macromol
118:671–675
75. Bartesaghi A, Aguerrebere C, Falconieri V, Banerjee S, Earl LA, Zhu X, Grigorieff N,
Milne JLS, Sapiro G, Wu X, Subramaniam S (2018) Atomic resolution cryo-EM structure of
beta-galactosidase. Structure 26(848–856):e3
76. Penczek PA (2010) Resolution measures in molecular electron microscopy. Methods
Enzymol 482:73–100
77. Harauz G, van Heel M (1986) Exact filters for general geometry three-dimensional
reconstruction. Optik 73:146–156
78. van Heel M, Schatz M (2005) Fourier shell correlation threshold criteria. J Struct Biol
151:250–262
79. Rosenthal PB, Henderson R (2003) Optimal determination of particle orientation, absolute
hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol 333:721–745
80. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z,
Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB,
Rossmann MG, Schmid MF, Schroder GF, Steven AC, Stokes DL, Westbrook JD,
Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL (2012)
Outcome of the first electron microscopy validation task force meeting. Structure 20:205–214
398
R. Natesh