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68. Elofsson A, Joo K, Keasar C et al (2018) Methods for estimation of model accuracy in
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69. Joseph AP, Polles G, Alber F et al (2017) Integrative modelling of cellular assemblies. Curr
Opin Struct Biol 46:102–109
70. Bullock JMA, Schwab J, Thalassinos K et al
(2016) The importance of non-accessible
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from crosslinking mass spectrometry. Mol Cell
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71. Bullock JMA, Thalassinos K, Topf M (2018)
Jwalk and MNXL web server: model validation
using restraints from crosslinking mass spectrometry. Bioinformatics 34:3584–3585
72. Bullock JMA, Sen N, Thalassinos K et al
(2018) Modeling protein complexes using
restraints from crosslinking mass spectrometry.
Structure 26:1015–1024.e2
73. Barad BA, Echols N, Wang RY-R et al (2015)
EMRinger: side chain–directed model and map
validation for 3D cryo-electron microscopy.
Nat Methods 12:943–946
74. Afonine PV, Klaholz BP, Moriarty NW et al
(2018) New tools for the analysis and validation of cryo-EM maps and atomic models. Acta
Crystallogr Sect Struct Biol 74:814–840
75. Chen VB, Arendall WB, Headd JJ et al (2010)
MolProbity: all-atom structure validation for
macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21
76. Atherton J, Jiang K, Stangier MM et al (2017)
A structural model for microtubule minus-end
recognition and protection by CAMSAP proteins. Nat Struct Mol Biol 24:931–943
77. Richardson JS, Williams CJ, Hintze BJ et al
(2018) Model validation: local diagnosis, correction and when to quit. Acta Crystallogr Sect
Struct Biol 74:132–142
78. Webb B, Sali A (2014) Protein structure modeling with MODELLER. In: Kihara D
(ed) Protein structure prediction. Springer,
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3D structure prediction. BMC Bioinformatics
9:40
80. Peng J, Xu J (2011) Raptorx: exploiting structure information for protein alignment by statistical inference. Proteins Struct Funct
Bioinforma 79:161–171
81. Schaarschmidt J, Monastyrskyy B, Kryshtafovych A et al (2018) Assessment of contact predictions in CASP12: co-evolution and deep
learning coming of age. Proteins Struct Funct
Bioinforma 86:51–66
82. Trott O, Olson AJ (2010) AutoDock Vina:
improving the speed and accuracy of docking
with a new scoring function, efficient optimization, and multithreading. J Comput Chem
31:455–461
83. Burnley T, Palmer CM, Winn M (2017)
Recent developments in the CCP-EM software
suite. Acta Crystallogr Sect Struct Biol
73:469–477
84. Jones A, Bland-Hawthorn J, Shopbell P (1995)
Towards a general definition for spectroscopic
resolution, In: Astronomical data analysis software and systems IV. ASP Conf Ser 77:503
85. Liao HY, Frank J (2010) Definition and estimation of resolution in single-particle reconstructions. Structure 18:768–775
86. Chaco ´n P, Wriggers W (2002) Multiresolution contour-based fitting of macromolecular structures. J Mol Biol 317:375–384
CryoEM Density Fitting and Validation
223
(2017) ProQ3D: improved model quality
assessments using deep learning. Bioinformatics 33:1578–1580
68. Elofsson A, Joo K, Keasar C et al (2018) Methods for estimation of model accuracy in
CASP12. Proteins Struct Funct Bioinforma
86:361–373
69. Joseph AP, Polles G, Alber F et al (2017) Integrative modelling of cellular assemblies. Curr
Opin Struct Biol 46:102–109
70. Bullock JMA, Schwab J, Thalassinos K et al
(2016) The importance of non-accessible
crosslinks and solvent accessible surface distance in modeling proteins with restraints
from crosslinking mass spectrometry. Mol Cell
Proteomics 15:2491–2500
71. Bullock JMA, Thalassinos K, Topf M (2018)
Jwalk and MNXL web server: model validation
using restraints from crosslinking mass spectrometry. Bioinformatics 34:3584–3585
72. Bullock JMA, Sen N, Thalassinos K et al
(2018) Modeling protein complexes using
restraints from crosslinking mass spectrometry.
Structure 26:1015–1024.e2
73. Barad BA, Echols N, Wang RY-R et al (2015)
EMRinger: side chain–directed model and map
validation for 3D cryo-electron microscopy.
Nat Methods 12:943–946
74. Afonine PV, Klaholz BP, Moriarty NW et al
(2018) New tools for the analysis and validation of cryo-EM maps and atomic models. Acta
Crystallogr Sect Struct Biol 74:814–840
75. Chen VB, Arendall WB, Headd JJ et al (2010)
MolProbity: all-atom structure validation for
macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66:12–21
76. Atherton J, Jiang K, Stangier MM et al (2017)
A structural model for microtubule minus-end
recognition and protection by CAMSAP proteins. Nat Struct Mol Biol 24:931–943
77. Richardson JS, Williams CJ, Hintze BJ et al
(2018) Model validation: local diagnosis, correction and when to quit. Acta Crystallogr Sect
Struct Biol 74:132–142
78. Webb B, Sali A (2014) Protein structure modeling with MODELLER. In: Kihara D
(ed) Protein structure prediction. Springer,
New York, NY, pp 1–15
79. Zhang Y (2008) I-TASSER server for protein
3D structure prediction. BMC Bioinformatics
9:40
80. Peng J, Xu J (2011) Raptorx: exploiting structure information for protein alignment by statistical inference. Proteins Struct Funct
Bioinforma 79:161–171
81. Schaarschmidt J, Monastyrskyy B, Kryshtafovych A et al (2018) Assessment of contact predictions in CASP12: co-evolution and deep
learning coming of age. Proteins Struct Funct
Bioinforma 86:51–66
82. Trott O, Olson AJ (2010) AutoDock Vina:
improving the speed and accuracy of docking
with a new scoring function, efficient optimization, and multithreading. J Comput Chem
31:455–461
83. Burnley T, Palmer CM, Winn M (2017)
Recent developments in the CCP-EM software
suite. Acta Crystallogr Sect Struct Biol
73:469–477
84. Jones A, Bland-Hawthorn J, Shopbell P (1995)
Towards a general definition for spectroscopic
resolution, In: Astronomical data analysis software and systems IV. ASP Conf Ser 77:503
85. Liao HY, Frank J (2010) Definition and estimation of resolution in single-particle reconstructions. Structure 18:768–775
86. Chaco ´n P, Wriggers W (2002) Multiresolution contour-based fitting of macromolecular structures. J Mol Biol 317:375–384
CryoEM Density Fitting and Validation
223