4. Connelly CM, Moon MH, Schneekloth JS
(2016) The emerging role of RNA as a therapeutic target for small molecules. Cell Chem
Biol 23:1077–1090
5. Collaborative Computational Project, Number
4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol
Crystallogr D50:760–763
6. Emsley P, Cowtan K (2004) Coot: modelbuilding tools for molecular graphics. Acta
Crystallogr
D
Biol
Crystallogr
D60:2126–2132
7. Emsley P, Lohkamp B, Scott WG et al (2010)
Features and development of Coot. Acta Crystallogr D Biol Crystallogr D66:486–501
8. Chojnowski G, Walen ´ T, Bujnicki JM (2014)
RNA Bricks—a database of RNA 3D motifs
and their interactions. Nucleic Acids Res 42:
D123–D131
9. Petrov AI, Zirbel CL, Leontis NB (2013)
Automated classification of RNA 3D motifs
and the RNA 3D Motif Atlas. RNA
19:1327–1340
10. Popenda M, Szachniuk M, Blazewicz M et al
(2010) RNA FRABASE 2.0: an advanced
web-accessible database with the capacity to
search the three-dimensional fragments within
RNA structures. BMC Bioinformatics 11:231
11. Pan X, Shen HB (2018) Predicting
RNA-protein binding sites and motifs through
combining local and global deep convolutional
neural
networks.
Bioinformatics
34:3427–3436
12. Tuszynska I, Magnus M, Jonak K et al (2015)
NPDock: a web server for protein–nucleic acid
docking. Nucleic Acids Res 43(W1):
W425–W430
13. Chauvot de Beauchene I, de Vries SJ, Zacharias
M (2016) Fragment-based modelling of single
stranded RNA bound to RNA recognition
motif containing proteins. Nucleic Acids Res
44:4565–4580
14. Rio DC (2014) Electrophoretic mobility shift
assays for RNA-protein complexes. Cold
Spring Harb Protoc 2014:435–440
15. Oubridge C, Ito N, Teo CH et al (1995) Crystallisation of RNA-protein complexes. II. The
application of protein engineering for crystallisation of the U1A protein-RNA complex. J
Mol Biol 249:409–423
16. Obayashi E, Oubridge C, Krummel DP et al
(2007) Crystallization of RNA-Protein complexes. Methods Mol Biol 363:259–276
17. Yakhnin AV, Yakhnin H, Babitzke P (2012) Gel
mobility shift assays to detect protein-RNA
interactions. Methods Mol Biol 905:201–211
18. Ke A, Doudna JA (2004) Crystallization of
RNA and RNA–protein complexes. Methods
34:408–414
19. Newman J, Egan D, Walter TS et al (2005)
Towards rationalization of crystallization
screening for small- to medium-sized academic
laboratories: the PACT/JCSG+ strategy. Acta
Crystallogr
D
Biol
Crystallogr
D61:1426–1431
20. Leslie AGW (1992) Recent changes to the
MOSFLM package for processing film and
image plate data. Jnt CCP4/ESF-EACMB
Newslett Protein Crystallogr 26
21. Potterton E, Briggs P, Turkenburg M et al
(2003) A graphical user interface to the CCP4
program suite. Acta Crystallogr D Biol Crystallogr D59:1131–1137
22. Winter (2010) xia2: an expert system for macromolecular crystallography data reduction. J
Appl Crystallogr 43:186–190
23. Chojnowski G, Bujnicki JM, Bochtler M
(2012) RIBER/DIBER: a software suite for
crystal content analysis in the studies of
protein-nucleic acid complexes. Bioinformatics
28:880–881
24. Waterhouse A, Bertoni M, Bienert S et al
(2018) SWISS-MODEL: homology modelling
of protein structures and complexes. Nucleic
Acids Res 46(W1):W296–W303
25. Yang J, Yan R, Roy A et al (2015) The
I-TASSER suite: protein structure and function
prediction. Nat Methods 12:7–8
26. McCoy AJ, Grosse-Kunstleve RW, Adams PD
et al (2007) Phaser crystallographic software. J
Appl Crystallogr 40:658–674
27. Adams PD, Afonine PV, Bunko ´ czi G et al
(2010) PHENIX: a comprehensive Pythonbased system for macromolecular structure
solution. Acta Crystallogr D Biol Crystallogr
D66:213–221
28. Keating KS, Pyle AM (2012) RCrane: semiautomated RNA model building. Acta Crystallogr D Biol Crystallogr 68:985–995
29. Davis IW, Leaver-Fay A, Chen VB et al (2007)
MolProbity: all-atom contacts and structure
validation for proteins and nucleic acids.
Nucleic Acids Res 35:W375–W383
30. Kru ¨ger DM, Neubacher S, Grossmann TN
(2018) Protein-RNA interactions: structural
characteristics and hotspot amino acids. RNA
24:1457–1465
31. Chen WF, Rety S, Guo HL et al (2018) Molecular mechanistic insights into Drosophila
DHX36-mediated G-quadruplex unfolding: a
structure-based model. Structure 26:403–415
446
Andrew P. Turnbull and Xiaoqiu Wu
(2016) The emerging role of RNA as a therapeutic target for small molecules. Cell Chem
Biol 23:1077–1090
5. Collaborative Computational Project, Number
4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol
Crystallogr D50:760–763
6. Emsley P, Cowtan K (2004) Coot: modelbuilding tools for molecular graphics. Acta
Crystallogr
D
Biol
Crystallogr
D60:2126–2132
7. Emsley P, Lohkamp B, Scott WG et al (2010)
Features and development of Coot. Acta Crystallogr D Biol Crystallogr D66:486–501
8. Chojnowski G, Walen ´ T, Bujnicki JM (2014)
RNA Bricks—a database of RNA 3D motifs
and their interactions. Nucleic Acids Res 42:
D123–D131
9. Petrov AI, Zirbel CL, Leontis NB (2013)
Automated classification of RNA 3D motifs
and the RNA 3D Motif Atlas. RNA
19:1327–1340
10. Popenda M, Szachniuk M, Blazewicz M et al
(2010) RNA FRABASE 2.0: an advanced
web-accessible database with the capacity to
search the three-dimensional fragments within
RNA structures. BMC Bioinformatics 11:231
11. Pan X, Shen HB (2018) Predicting
RNA-protein binding sites and motifs through
combining local and global deep convolutional
neural
networks.
Bioinformatics
34:3427–3436
12. Tuszynska I, Magnus M, Jonak K et al (2015)
NPDock: a web server for protein–nucleic acid
docking. Nucleic Acids Res 43(W1):
W425–W430
13. Chauvot de Beauchene I, de Vries SJ, Zacharias
M (2016) Fragment-based modelling of single
stranded RNA bound to RNA recognition
motif containing proteins. Nucleic Acids Res
44:4565–4580
14. Rio DC (2014) Electrophoretic mobility shift
assays for RNA-protein complexes. Cold
Spring Harb Protoc 2014:435–440
15. Oubridge C, Ito N, Teo CH et al (1995) Crystallisation of RNA-protein complexes. II. The
application of protein engineering for crystallisation of the U1A protein-RNA complex. J
Mol Biol 249:409–423
16. Obayashi E, Oubridge C, Krummel DP et al
(2007) Crystallization of RNA-Protein complexes. Methods Mol Biol 363:259–276
17. Yakhnin AV, Yakhnin H, Babitzke P (2012) Gel
mobility shift assays to detect protein-RNA
interactions. Methods Mol Biol 905:201–211
18. Ke A, Doudna JA (2004) Crystallization of
RNA and RNA–protein complexes. Methods
34:408–414
19. Newman J, Egan D, Walter TS et al (2005)
Towards rationalization of crystallization
screening for small- to medium-sized academic
laboratories: the PACT/JCSG+ strategy. Acta
Crystallogr
D
Biol
Crystallogr
D61:1426–1431
20. Leslie AGW (1992) Recent changes to the
MOSFLM package for processing film and
image plate data. Jnt CCP4/ESF-EACMB
Newslett Protein Crystallogr 26
21. Potterton E, Briggs P, Turkenburg M et al
(2003) A graphical user interface to the CCP4
program suite. Acta Crystallogr D Biol Crystallogr D59:1131–1137
22. Winter (2010) xia2: an expert system for macromolecular crystallography data reduction. J
Appl Crystallogr 43:186–190
23. Chojnowski G, Bujnicki JM, Bochtler M
(2012) RIBER/DIBER: a software suite for
crystal content analysis in the studies of
protein-nucleic acid complexes. Bioinformatics
28:880–881
24. Waterhouse A, Bertoni M, Bienert S et al
(2018) SWISS-MODEL: homology modelling
of protein structures and complexes. Nucleic
Acids Res 46(W1):W296–W303
25. Yang J, Yan R, Roy A et al (2015) The
I-TASSER suite: protein structure and function
prediction. Nat Methods 12:7–8
26. McCoy AJ, Grosse-Kunstleve RW, Adams PD
et al (2007) Phaser crystallographic software. J
Appl Crystallogr 40:658–674
27. Adams PD, Afonine PV, Bunko ´ czi G et al
(2010) PHENIX: a comprehensive Pythonbased system for macromolecular structure
solution. Acta Crystallogr D Biol Crystallogr
D66:213–221
28. Keating KS, Pyle AM (2012) RCrane: semiautomated RNA model building. Acta Crystallogr D Biol Crystallogr 68:985–995
29. Davis IW, Leaver-Fay A, Chen VB et al (2007)
MolProbity: all-atom contacts and structure
validation for proteins and nucleic acids.
Nucleic Acids Res 35:W375–W383
30. Kru ¨ger DM, Neubacher S, Grossmann TN
(2018) Protein-RNA interactions: structural
characteristics and hotspot amino acids. RNA
24:1457–1465
31. Chen WF, Rety S, Guo HL et al (2018) Molecular mechanistic insights into Drosophila
DHX36-mediated G-quadruplex unfolding: a
structure-based model. Structure 26:403–415
446
Andrew P. Turnbull and Xiaoqiu Wu