48. Boccaletto, P., Machnicka, M. A., Purta, E., Piatkowski, P., Baginski, B., Wirecki, T. K.,
et al. (2018). MODOMICS: A database of RNA modification pathways. Nucleic Acids
Research, 46(D1), D303–D307.
49. Schnabl, J., Suter, P., & Sigel, R. K. (2012). MINAS–a database of metal ions in nucleic
acids. Nucleic Acids Research, 40(Database issue), D434–D438.
50. Kirsanov, D. D., Zanegina, O. N., Aksianov, E. A., Spirin, S. A., Karyagina, A. S., &
Alexeevski, A. V. (2013). NPIDB: Nucleic acid-protein interaction database. Nucleic Acids
Research, 41(Database issue), D517–D523.
51. Tus, A., Rakipovic, A., Peretin, G., Tomic, S., & Sikic, M. (2012). BioMe: Biologically
relevant metals. Nucleic Acids Research, 40(Web Server issue), W352–W357.
52. Mehta, A., Sonam, S., Gouri, I., Loharch, S., Sharma, D. K., & Parkesh, R. (2014).
SMMRNA: A database of small molecule modulators of RNA. Nucleic Acids Research, 42
(Database issue), D132–D141.
53. Tan, L., Li, Y., Drake, T. J., Moroz, L., Wang, K., Li, J., et al. (2005). Molecular beacons for
bioanalytical applications. Analyst, 130(7), 1002–1005.
54. Lu, X. J., & Olson, W. K. (2008). 3DNA: A versatile, integrated software system for the
analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature
Protocols, 3(7), 1213–1227.
55. Magnus, M., Boniecki, M. J., Dawson, W., & Bujnicki, J. M. (2016). SimRNAweb: A web
server for RNA 3D structure modeling with optional restraints. Nucleic Acids Research, 44
(W1), W315–W319.
56. Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., et al.
(2011). NUPACK: Analysis and design of nucleic acid systems. Journal of Computational
Chemistry, 32(1), 170–173.
57. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Research, 31(13), 3406–3415.
58. Westhof, E., Masquida, B., & Jossinet, F. (2011). Predicting and modeling RNA architecture.
Cold Spring Harbor Perspectives in Biology, 3(2), a003632.
59. Hofacker, I. L. (2003). Vienna RNA secondary structure server. Nucleic Acids Research, 31
(13), 3429–3431.
60. Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K. J., Lukasiak, P., Bartol, N., et al.
(2012). Automated 3D structure composition for large RNAs. Nucleic Acids Research, 40
(14), e112.
61. Chen, V. B., Arendall, W. B., 3rd, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G.
J., et al. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 1), 12–21.
62. Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., et al.
(2005). The Amber biomolecular simulation programs. Computers & Chemistry, 26(16),
1668–1688.
63. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H.
J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16),
1701–1718.
64. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., et al. (2005).
Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16),
1781–1802.
65. Li, L., Li, C., Sarkar, S., Zhang, J., Witham, S., Zhang, Z., et al. (2012). DelPhi: A
comprehensive suite for DelPhi software and associated resources. BMC Biophysics, 14(5), 9.
66. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., et al.
(2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor
flexibility. Journal of Computational Chemistry, 30(16), 2785–2791 (Allen, W. J., Balius, T.
E., Mukherjee, S., Brozell, S. R., Moustakas, D. T., Lang, P. T., Case, D. A.).
67. Kuntz, I. D., & Rizzo, R. C. (2015). DOCK 6: Impact of new features and current docking
performance. Journal of Computational Chemistry, 36(15), 1132–1156.
Computational Design of Nucleic Acid-Based Bioreceptor …
229
et al. (2018). MODOMICS: A database of RNA modification pathways. Nucleic Acids
Research, 46(D1), D303–D307.
49. Schnabl, J., Suter, P., & Sigel, R. K. (2012). MINAS–a database of metal ions in nucleic
acids. Nucleic Acids Research, 40(Database issue), D434–D438.
50. Kirsanov, D. D., Zanegina, O. N., Aksianov, E. A., Spirin, S. A., Karyagina, A. S., &
Alexeevski, A. V. (2013). NPIDB: Nucleic acid-protein interaction database. Nucleic Acids
Research, 41(Database issue), D517–D523.
51. Tus, A., Rakipovic, A., Peretin, G., Tomic, S., & Sikic, M. (2012). BioMe: Biologically
relevant metals. Nucleic Acids Research, 40(Web Server issue), W352–W357.
52. Mehta, A., Sonam, S., Gouri, I., Loharch, S., Sharma, D. K., & Parkesh, R. (2014).
SMMRNA: A database of small molecule modulators of RNA. Nucleic Acids Research, 42
(Database issue), D132–D141.
53. Tan, L., Li, Y., Drake, T. J., Moroz, L., Wang, K., Li, J., et al. (2005). Molecular beacons for
bioanalytical applications. Analyst, 130(7), 1002–1005.
54. Lu, X. J., & Olson, W. K. (2008). 3DNA: A versatile, integrated software system for the
analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nature
Protocols, 3(7), 1213–1227.
55. Magnus, M., Boniecki, M. J., Dawson, W., & Bujnicki, J. M. (2016). SimRNAweb: A web
server for RNA 3D structure modeling with optional restraints. Nucleic Acids Research, 44
(W1), W315–W319.
56. Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., et al.
(2011). NUPACK: Analysis and design of nucleic acid systems. Journal of Computational
Chemistry, 32(1), 170–173.
57. Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction.
Nucleic Acids Research, 31(13), 3406–3415.
58. Westhof, E., Masquida, B., & Jossinet, F. (2011). Predicting and modeling RNA architecture.
Cold Spring Harbor Perspectives in Biology, 3(2), a003632.
59. Hofacker, I. L. (2003). Vienna RNA secondary structure server. Nucleic Acids Research, 31
(13), 3429–3431.
60. Popenda, M., Szachniuk, M., Antczak, M., Purzycka, K. J., Lukasiak, P., Bartol, N., et al.
(2012). Automated 3D structure composition for large RNAs. Nucleic Acids Research, 40
(14), e112.
61. Chen, V. B., Arendall, W. B., 3rd, Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G.
J., et al. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica. Section D, Biological Crystallography, 66(Pt 1), 12–21.
62. Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., et al.
(2005). The Amber biomolecular simulation programs. Computers & Chemistry, 26(16),
1668–1688.
63. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H.
J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16),
1701–1718.
64. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., et al. (2005).
Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16),
1781–1802.
65. Li, L., Li, C., Sarkar, S., Zhang, J., Witham, S., Zhang, Z., et al. (2012). DelPhi: A
comprehensive suite for DelPhi software and associated resources. BMC Biophysics, 14(5), 9.
66. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., et al.
(2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor
flexibility. Journal of Computational Chemistry, 30(16), 2785–2791 (Allen, W. J., Balius, T.
E., Mukherjee, S., Brozell, S. R., Moustakas, D. T., Lang, P. T., Case, D. A.).
67. Kuntz, I. D., & Rizzo, R. C. (2015). DOCK 6: Impact of new features and current docking
performance. Journal of Computational Chemistry, 36(15), 1132–1156.
Computational Design of Nucleic Acid-Based Bioreceptor …
229