GroEL oligomers resolved by Cryo-EM. Proc
Natl Acad Sci 114:8259–8264
13. Estevez PA, Tesmer M, Perez CA et al (2009)
Normalized mutual information feature selection. IEEE Trans Neural Netw 20:189–201
14. Studholme C, Hill DLG, Hawkes DJ (1999)
An overlap invariant entropy measure of 3D
medical image alignment. Pattern Recogn
32:71–86
15. Kryshtafovych A, Malhotra S, Monastyrskyy B
et al (2019) Cryo-EM targets in CASP13:
overview and evaluation of results. Proteins
87:1128–1140
16. Joseph AP, Malhotra S, Burnley T et al (2016)
Refinement of atomic models in high resolution EM reconstructions using flex-EM and
local assessment. Methods 100:42–49
17. Farabella I, Vasishtan D, Joseph AP et al (2015)
TEMPy: a Python library for assessment of
three-dimensional electron microscopy density
fits. J Appl Crystallogr 48:1314–1323
18. Afonine PV, Poon BK, Read RJ et al (2018)
Real-space refinement in PHENIX for cryoEM and crystallography. Acta Crystallogr Sect
Struct Biol 74:531–544
19. Emsley P, Lohkamp B, Scott WG et al (2010)
Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501
20. Song Y, DiMaio F, Wang RY-R et al (2013)
High-resolution comparative modeling with
RosettaCM. Structure 21:1735–1742
21. Waterhouse A, Bertoni M, Bienert S et al
(2018) SWISS-MODEL: homology modelling
of protein structures and complexes. Nucleic
Acids Res 46:W296–W303
22. Atherton J, Yu I-MI-M, Cook A et al (2017)
The divergent mitotic kinesin MKLP2 exhibits
atypical structure and mechanochemistry. elife
6:e27793
23. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition
of hydrogen-bonded and geometrical features.
Biopolymers 22:2577–2637
24. Benkert P, Biasini M, Schwede T (2011)
Toward the estimation of the absolute quality
of individual protein structure models. Bioinformatics 27:343–350
25. Topf M, Baker ML, John B et al (2005) Structural characterization of components of protein
assemblies by comparative modeling and electron
cryo-microscopy.
J
Struct
Biol
149:191–203
26. Pintilie GD, Zhang J, Goddard TD et al (2010)
Quantitative analysis of cryo-EM density map
segmentation by watershed and scale-space
filtering, and fitting of structures by alignment
to regions. J Struct Biol 170:427–438
27. Wu X, Milne JLS, Borgnia MJ et al (2003) A
core-weighted fitting method for docking
atomic structures into low-resolution maps:
application to cryo-electron microscopy. J
Struct Biol 141:63–76
28. Kim SJ, Fernandez-Martinez J, Nudelman I
et al (2018) Integrative structure and functional anatomy of a nuclear pore complex.
Nature 555:475–482
29. Kuzu G, Keskin O, Nussinov R et al (2016)
PRISM-EM: template interface-based modelling of multi-protein complexes guided by
cryo-electron microscopy density maps. Acta
Crystallogr Sect Struct Biol 72:1137–1148
30. Chandramouli P, Topf M, Me ´ne ´tret J-F et al
(2008) Structure of the mammalian 80S ribosome at 8.7 A ˚ resolution. Structure
16:535–548
31. Taylor DJ, Devkota B, Huang AD et al (2009)
Comprehensive molecular structure of the
eukaryotic ribosome. Structure 17:1591–1604
32. Kawabata T (2008) Multiple subunit fitting
into a low-resolution density map of a macromolecular complex using a Gaussian mixture
model. Biophys J 95:4643–4658
33. Tjioe E, Lasker K, Webb B et al (2011) MultiFit: a web server for fitting multiple protein
structures into their electron microscopy density map. Nucleic Acids Res 39:W167–W170
34. Pandurangan AP, Vasishtan D, Alber F et al
(2015) γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly
using a genetic algorithm. Structure
23:2365–2376
35. Zhang S, Vasishtan D, Xu M et al (2010) A fast
mathematical programming procedure for
simultaneous fitting of assembly components
into cryoEM density maps. Bioinformatics
26:261–268
36. Zeev-Ben-Mordehai T, Vasishtan D, Herna ´ndez Dura ´n A et al (2016) Two distinct trimeric
conformations of natively membrane-anchored
full-length herpes simplex virus 1 glycoprotein
B. Proc Natl Acad Sci 113:4176–4181
37. Baker ML, Jiang W, Wedemeyer WJ et al
(2006) Ab initio modeling of the Herpesvirus
VP26 Core domain assessed by CryoEM density. PLoS Comput Biol 2:12
38. Sachse C, Chen JZ, Coureux P-D et al (2007)
High-resolution Electron microscopy of helical
specimens: a fresh look at tobacco mosaic virus.
J Mol Biol 371:812–835
CryoEM Density Fitting and Validation
221
Natl Acad Sci 114:8259–8264
13. Estevez PA, Tesmer M, Perez CA et al (2009)
Normalized mutual information feature selection. IEEE Trans Neural Netw 20:189–201
14. Studholme C, Hill DLG, Hawkes DJ (1999)
An overlap invariant entropy measure of 3D
medical image alignment. Pattern Recogn
32:71–86
15. Kryshtafovych A, Malhotra S, Monastyrskyy B
et al (2019) Cryo-EM targets in CASP13:
overview and evaluation of results. Proteins
87:1128–1140
16. Joseph AP, Malhotra S, Burnley T et al (2016)
Refinement of atomic models in high resolution EM reconstructions using flex-EM and
local assessment. Methods 100:42–49
17. Farabella I, Vasishtan D, Joseph AP et al (2015)
TEMPy: a Python library for assessment of
three-dimensional electron microscopy density
fits. J Appl Crystallogr 48:1314–1323
18. Afonine PV, Poon BK, Read RJ et al (2018)
Real-space refinement in PHENIX for cryoEM and crystallography. Acta Crystallogr Sect
Struct Biol 74:531–544
19. Emsley P, Lohkamp B, Scott WG et al (2010)
Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501
20. Song Y, DiMaio F, Wang RY-R et al (2013)
High-resolution comparative modeling with
RosettaCM. Structure 21:1735–1742
21. Waterhouse A, Bertoni M, Bienert S et al
(2018) SWISS-MODEL: homology modelling
of protein structures and complexes. Nucleic
Acids Res 46:W296–W303
22. Atherton J, Yu I-MI-M, Cook A et al (2017)
The divergent mitotic kinesin MKLP2 exhibits
atypical structure and mechanochemistry. elife
6:e27793
23. Kabsch W, Sander C (1983) Dictionary of protein secondary structure: pattern recognition
of hydrogen-bonded and geometrical features.
Biopolymers 22:2577–2637
24. Benkert P, Biasini M, Schwede T (2011)
Toward the estimation of the absolute quality
of individual protein structure models. Bioinformatics 27:343–350
25. Topf M, Baker ML, John B et al (2005) Structural characterization of components of protein
assemblies by comparative modeling and electron
cryo-microscopy.
J
Struct
Biol
149:191–203
26. Pintilie GD, Zhang J, Goddard TD et al (2010)
Quantitative analysis of cryo-EM density map
segmentation by watershed and scale-space
filtering, and fitting of structures by alignment
to regions. J Struct Biol 170:427–438
27. Wu X, Milne JLS, Borgnia MJ et al (2003) A
core-weighted fitting method for docking
atomic structures into low-resolution maps:
application to cryo-electron microscopy. J
Struct Biol 141:63–76
28. Kim SJ, Fernandez-Martinez J, Nudelman I
et al (2018) Integrative structure and functional anatomy of a nuclear pore complex.
Nature 555:475–482
29. Kuzu G, Keskin O, Nussinov R et al (2016)
PRISM-EM: template interface-based modelling of multi-protein complexes guided by
cryo-electron microscopy density maps. Acta
Crystallogr Sect Struct Biol 72:1137–1148
30. Chandramouli P, Topf M, Me ´ne ´tret J-F et al
(2008) Structure of the mammalian 80S ribosome at 8.7 A ˚ resolution. Structure
16:535–548
31. Taylor DJ, Devkota B, Huang AD et al (2009)
Comprehensive molecular structure of the
eukaryotic ribosome. Structure 17:1591–1604
32. Kawabata T (2008) Multiple subunit fitting
into a low-resolution density map of a macromolecular complex using a Gaussian mixture
model. Biophys J 95:4643–4658
33. Tjioe E, Lasker K, Webb B et al (2011) MultiFit: a web server for fitting multiple protein
structures into their electron microscopy density map. Nucleic Acids Res 39:W167–W170
34. Pandurangan AP, Vasishtan D, Alber F et al
(2015) γ-TEMPy: simultaneous fitting of components in 3D-EM maps of their assembly
using a genetic algorithm. Structure
23:2365–2376
35. Zhang S, Vasishtan D, Xu M et al (2010) A fast
mathematical programming procedure for
simultaneous fitting of assembly components
into cryoEM density maps. Bioinformatics
26:261–268
36. Zeev-Ben-Mordehai T, Vasishtan D, Herna ´ndez Dura ´n A et al (2016) Two distinct trimeric
conformations of natively membrane-anchored
full-length herpes simplex virus 1 glycoprotein
B. Proc Natl Acad Sci 113:4176–4181
37. Baker ML, Jiang W, Wedemeyer WJ et al
(2006) Ab initio modeling of the Herpesvirus
VP26 Core domain assessed by CryoEM density. PLoS Comput Biol 2:12
38. Sachse C, Chen JZ, Coureux P-D et al (2007)
High-resolution Electron microscopy of helical
specimens: a fresh look at tobacco mosaic virus.
J Mol Biol 371:812–835
CryoEM Density Fitting and Validation
221