Coarse-grained modeling of RNA 3D structure

Methods

Volumn 103, Issue , 2016, Pages 138-156

  Dawson, Wayne K ^a   Maciejczyk, Maciej ^a,b   Jankowska, Elzbieta J ^a   Bujnicki, Janusz M ^a,c  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b UNIVERSITY OF WARMIA AND MAZURY IN OLSZTYN   (Poland)

^c ADAM MICKIEWICZ UNIVERSITY   (Poland)

Author keywords

Bioinformatics; Modeling; Molecular dynamics; Monte Carlo dynamics; RNA; Simulation; Structure

Indexed keywords

ALL ATOM MOLECULAR MECHANICS; COARSE GRAINED MOLECULAR MECHANICS; ELECTRON SPIN RESONANCE; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTON TRANSPORT; REVIEW; RNA ANALYSIS; RNA FOLDING; RNA PROCESSING; RNA STRUCTURE; CHEMISTRY; CONFORMATION; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; THERMODYNAMICS;

RNA;

BASE SEQUENCE; DATABASES, NUCLEIC ACID; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA; THERMODYNAMICS;

EID: 84964642759     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2016.04.026     Document Type: Review

References (197)

1. Gesteland R.F. The RNA World 2005, Cold Spring Harbor. third ed.
2. Serganov A., Nudler E. Cell 2013, 152:17-24.
3. Serganov A., Patel D.J. Curr. Opin. Struct. Biol. 2012, 22:279-286.
4. Doudna J.A. Nat. Struct. Biol. 2000, 7(Suppl):954-956.
5. Consortium T.R. Nucleic Acids Res. 2015, 43:D123-D129.
6. Magnus M., Matelska D., Lach G., Chojnowski G., Boniecki M.J., Purta E., Dawson W., Dunin-Horkawicz S., Bujnicki J.M. RNA Biol. 2014, 11:522-536.
7. Sim A.Y., Minary P., Levitt M. Curr. Opin. Struct. Biol. 2012, 22:273-278.
8. Laing C., Schlick T. Curr. Opin. Struct. Biol. 2011, 21:306-318.
9. Rother K., Rother M., Boniecki M., Puton T., Bujnicki J.M. J. Mol. Model. 2011, 17:2325-2336.
10. Dawson W.K., Bujnicki J.M. Curr. Opin. Struct. Biol. 2015, 37:22-28.
11. Green L., Kim C.H., Bustamante C., Tinoco I. J. Mol. Biol. 2008, 375:511-528.
12. Narayanan R., Velmurugu Y., Kuznetsov S.V., Ansari A. J. Am. Chem. Soc. 2011, 133:18767-18774.
13. Chen G., Wen J.D., Tinoco I. RNA 2007, 13:2175-2188.
14. Schlatterer J.C., Martin J.S., Laederach A., Brenowitz M. PLoS One 2014, 9:e85041.
15. Shaw D.E., O'Dror R., Salmon J.K., Grossman J.P., Mackenzie K.M., Bank J.A., Young C., Deneroff M.M., Batson B., Bowers K.J., Chow E., Eastwood M.P., Lerardi D.J., Klepeis J.L., Kuskin J.S., Larson R.H., Lindorff-Larsen K., Maragakis P., Moraes M.A., Piana S., Shan Y., Towles B. Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09) 2009, ACM.
16. Sponer J., Sponer J.E., Mladek A., Banas P., Jurecka P., Otyepka M. Methods 2013, 64:3-11.
17. Noid W.G. J. Chem. Phys. 2013, 139:090901.
18. Noid W.G. Methods Mol. Biol. 2013, 924:487-531.
19. Noid W.G. Biomol Sim: Meth Prot, Meth Mol Biol 2012, Springer Science + Business Media, New York. L. Monticelli, E. Salonen (Eds.).
20. Matysiak S., Clementi C. Arch. Biochem. Biophys. 2008, 469:29-33.
21. Tozzini V. Q. Rev. Biophys. 2010, 43:333-371.
22. Saunders M.G., Voth G.A. Annu. Rev. Biophys. 2013, 42:73-93.
23. Kamerlin S.C., Vicatos S., Dryga A., Warshel A. Annu. Rev. Phys. Chem. 2011, 62:41-64.
24. Jonikas M.A., Radmer R.J., Laederach A., Das R., Pearlman S., Herschlag D., Altman R.B. RNA 2009, 15:189-199.
25. Olson W.K., Zhurkin V.B. Curr. Opin. Struct. Biol. 2000, 10:286-297.
26. Reblova K., Sponer J., Lankas F. Nucleic Acids Res. 2012, 40:6290-6303.
27. Munteanu M.G., Vlahovicek K., Parthasarathy S., Simon I., Pongor S. Trends Biochem. Sci. 1998, 23:341-347.
28. Balaeff A., Mahadevan L., Schulten K. Phys. Rev. E 2006, 73:031919.
29. Swigon D., Coleman B.D., Tobias I. Biophys. J. 1998, 74:2515-2530.
30. Sponer J., Sponer J.E., Mladek A., Jurecka P., Banas P., Otyepka M. Biopolymers 2013, 99:978-988.
31. Banas P., Jurecka P., Walter N.G., Sponer J., Otyepka M. Methods 2009, 49:202-216.
32. Bala P., Grochowski P., Nowinski K., Lesyng B., McCammon J.A. Biophys. J. 2000, 79:1253-1262.
33. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A. J. Comput. Chem. 2004, 25:1157-1174.
34. Cornell W.D., Cieplak P., Bayly C.L., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. J. Am. Chem. Soc. 1995, 117:5179-5197.
35. Galindo-Murillo R., Roe D.R., Cheatham T.E. Biochim. Biophys. Acta 2015, 1850:1041-1058.
36. MacKerell A.D., Banavali N., Foloppe N. Biopolymers 2000, 56:257-265.
37. Oostenbrink C., Villa A., Mark A.E., van Gunsteren W.F. J. Comput. Chem. 2004, 25:1656-1676.
38. Halgren T.A. J. Comput. Chem. 1996, 17:490-519.
39. Jorgensen W.L., Maxwell D.S., Tirada-Rives J. J. Am. Chem. Soc. 1996, 118:11225-11236.
40. Jorgensen W.L., Tirada-Rives J. J. Am. Chem. Soc. 1988, 110:1657-1666.
41. Sippl M.J. J. Comput. Aided Mol. Des. 1993, 7:473-501.
42. Shcherbakova I., Mitra S., Laederach A., Brenowitz M. Curr. Opin. Chem. Biol. 2008, 12:655-666.
43. Hyeon C., Thirumalai D. Biophys. J. 2006, 90:3410-3427.
44. Isambert H. Methods 2009, 49:189-196.
45. Xayaphoummine A., Viasnoff V., Harlepp S., Isambert H. Nucleic Acids Res. 2007, 35:614-622.
46. Xayaphoummine A., Bucher T., Isambert H. Nucleic Acids Res. 2005, 33:W605-W610.
47. Xayaphoummine A., Bucher T., Thalmann F., Isambert H. Proc. Natl. Acad. Sci. 2003, 100:15310-15314.
48. Sambriski E.J., Ortiz V., de Pablo J.J. J. Phys. Condens. Matter 2009, 21:034105.
49. Ouldridge T.E., Sulc P., Romano F., Doye J.P., Louis A.A. Nucleic Acids Res. 2013, 41:8886-8895.
50. Sulc P., Romano F., Ouldridge T.E., Doye J.P., Louis A.A. J. Chem. Phys. 2014, 140:235102.
51. Cragnolini T., Derreumaux P., Pasquali S. J. Phys. Chem. B 2013, 117:8047-8060.
52. Maciejczyk M., Spasic A., Liwo A., Scheraga H.A. J. Chem. Theory Comput. 2014, 10:5020-5035.
53. He Y., Maciejczyk M., Oldziej S., Scheraga H.A., Liwo A. Phys. Rev. Lett. 2013, 110:098101.
54. Pearlman D.A., Case D.A., Caldwell J.W., Ross W.S., Cheatham T.E., Debolt S., Ferguson D., Seibel G., Kollman P. Comput. Phys. Commun. 1995, 91:1-41.
55. Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. J. Comput. Chem. 2005, 26:1668-1688.
56. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. J. Comput. Chem. 1983, 4:187-217.
57. Pronk S., Pall S., Schulz R., Larsson P., Bjelkmar P., Apostolov R., Shirts M.R., Smith J.C., Kasson P.M., van der Spoel D., Hess B., Lindahl E. Bioinformatics 2013, 29:845-854.
58. Berendsen H.J.C., Vanderspoel D., Vandrunen R. Comput. Phys. Commun. 1995, 91:43-56.
59. Ponder J.W., Richards F.M. J. Comput. Chem. 1987, 8:1016-1024.
60. Ren P., Wu C., Ponder J.W. J. Chem. Theory Comput. 2011, 7:3143-3161.
61. Kale L., Skeel R., Bhandarkar M., Brunner R., Gursoy A., Krawetz N., Phillips J., Shinozaki A., Varadarajan K., Schulten K. J. Comput. Phys. 1999, 151:283-312.
62. Nelson M.T., Humphrey W., Gursoy A., Dalke A., Kale L.V., Skeel R.D., Schulten K. Int. J. Supercomput. Appl. High Perform. Comput. 1996, 10:251-268.
63. Weiner S.J., Kollman P.A., Nguyen D.T., Case D.A. J. Comput. Chem. 1986, 7:230-252.
64. MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M. J. Phys. Chem. B 1998, 102:3586-3616.
65. Devlin J.P., Hisatsune I.C. Spectrochim. Acta 1961, 17:218-225.
66. Morgado C.A., Svozil D., Turner D.H., Sponer J. Phys. Chem. Chem. Phys. 2012, 14:12580-12591.
67. Srinivasan A.R., Sauers R.R., Fenley M.O., Boschitsch A.H., Matsumoto A., Colasanti A.V., Olson W.K. Biophys. Rev. 2009, 1:13-20.
68. Seetin M.G., Mathews D.H. J. Comput. Chem. 2011.
69. Tsui V., Case D.A. Biopolymers 2001, 56:275-291.
70. Das R., Kudaravalli M., Jonikas M., Laederach A., Fong R., Schwans J.P., Baker D., Piccirilli J.A., Altman R.B., Herschlag D. Proc. Natl. Acad. Sci. 2008, 105:4144-4149.
71. Das R., Karanicolas J., Baker D. Nat. Methods 2010, 7:291-294.
72. Capriotti E., Norambuena T., Marti-Renom M.A., Melo F. Bioinformatics 2011, 27:1086-1093.
73. Cheng C.Y., Chou F.C., Das R. Methods Enzymol. 2015, 553:35-64.
74. Das R., Baker D. Proc. Natl. Acad. Sci. 2007, 104:14664-14669.
75. Parisien M., Major F. Nature 2008, 452:51-55.
76. Reinharz V., Major F., Waldispuhl J. Bioinformatics 2012, 28:i207-i214.
77. Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. J. Am. Chem. Soc. 1990, 112:6127-6129.
78. Honig B., Sharp K., Yang A.S. J. Phys. Chem. 1993, 97:1101-1109.
79. Deng N.J., Cieplak P. J. Chem. Theory Comput. 2007, 3:1435-1450.
80. Srinivasan J., Cheatham T.E., Cieplak P., Kollman P.A., Case D.A. J. Am. Chem. Soc. 1998, 120:9401-9409.
81. Besseova I., Reblova K., Leontis N.B., Sponer J. Nucleic Acids Res. 2010, 38:6247-6264.
82. Florian J., Sponer J., Warshel A. J. Phys. Chem. B 1999, 103:884-892.
83. Svozil D., Hobza P., Sponer J. J. Phys. Chem. B 2010, 114:1191-1203.
84. Piana S., Klepeis J.L., Shaw D.E. Curr. Opin. Struct. Biol. 2014, 24:98-105.
85. Knight J.L., Brooks C.L. J. Comput. Chem. 2011, 32:2909-2923.
86. McDowell S.E., Spackova N., Sponer J., Walter N.G. Biopolymers 2007, 85:169-184.
87. Harris R.C., Pettitt B.M. J. Chem. Theory Comput. 2015, 11:4593-4600.
88. Liu Y., Haddadian E., Sosnick T.R., Freed K.F., Gong H. Biophys. J. 2013, 105:1248-1257.
89. Kleinjung J., Fraternali F. Curr. Opin. Struct. Biol. 2014, 25:126-134.
90. Kamerlin S.C., Haranczyk M., Warshel A. ChemPhysChem 2009, 10:1125-1134.
91. Dlugosz M., Antosiewicz J.M. Chem. Phys. 2004, 302:161-170.
92. Dlugosz M., Antosiewicz J.M., Robertson A.D. Phys. Rev. E 2004, 69.
93. Dlugosz M., Antosiewicz J.M. Z. Naturforsch. A 2004, 59:873-874.
94. Goh G.B., Hulbert B.S., Zhou H., Brooks C.L. Proteins 2014, 82:1319-1331.
95. Goh G.B., Knight J.L., Brooks C.L. J. Chem. Theory Comput. 2012, 8:36-46.
96. Goh G.B., Knight J.L., Brooks C.L. J. Chem. Theory Comput. 2013, 9:935-943.
97. Yu H., Whitfield T.W., Harder E., Lamoureux G., Vorobyov I., Anisimov V.M., Mackerell A.D., Roux B. J. Chem. Theory Comput. 2010, 6:774-786.
98. Leontyev I., Stuchebrukhov A. Phys. Chem. Chem. Phys. 2011, 13:2613-2626.
99. Boniecki M.J., Lach G., Dawson W.K., Tomala K., Lukasz P., Soltysinski T., Rother K.M., Bujnicki J.M. Nucleic Acids Res. 2015, 10.1093/nar/gkv1479.
100. Ouldridge T.E., Louis A.A., Doye J.P. J. Chem. Phys. 2011, 134:085101.
101. Bowman J.C., Lenz T.K., Hud N.V., Williams L.D. Curr. Opin. Struct. Biol. 2012, 22:262-272.
102. Tozzini V. Acc. Chem. Res. 2010, 43:220-230.
103. de Jong D.H., Singh G., Bennett W.F.D., Arnarez C., Wassenaar T.A., Schafer L.V., Periole X., Tieleman D.P., Marrink S.J. J. Chem. Theory Comput. 2013, 9:687-697.
104. Marrink S.J., Tieleman D.P. Chem. Soc. Rev. 2013, 42:6801-6822.
105. Chen R., Weng Z. Proteins 2003, 51:397-408.
106. Pierce B.G., Wiehe K., Hwang H., Kim B.H., Vreven T., Weng Z. Bioinformatics 2014, 30:1771-1773.
107. Chen R., Li L., Weng Z. Proteins 2003, 52:80-87.
108. Maciejczyk M., Spasic A., Liwo A., Scheraga H.A. J. Comput. Chem. 2010, 31:1644-1655.
109. Olson W.K., Flory P.J. Biopolymers 1972, 11:1-23.
110. Olson W.K., Flory P.J. Biopolymers 1972, 11:25-56.
111. Olson W.K., Flory P.J. Biopolymers 1972, 11:57-66.
112. Olson W.K. Macromolecules 1980, 13:721-728.
113. Murray L.J., Arendall W.B., Richardson D.C., Richardson J.S. Proc. Natl. Acad. Sci. 2003, 100:13904-13909.
114. Takasu A., Watanabe K., Kawai G. Nucleic Acids 2002, 21:449-462.
115. Saenger W. Principles of Nucleic Acid Structure 1984, Springer-Verlag, New York.
116. Duarte C.M., Wadley L.M., Pyle A.M. Nucleic Acids Res. 2003, 31:4755-4761.
117. Wadley L.M., Keating K.S., Duarte C.M., Pyle A.M. J. Mol. Biol. 2007, 372:942-957.
118. Duarte C.M., Pyle A.M. J. Mol. Biol. 1998, 284:1465-1478.
119. Liu L., Chen S.J. PLoS One 2012, 7.
120. Dawson W., Kawai G. J. Comput. Sci. Syst. Biol. 2009, 2:1-23.
121. Cao S., Chen S.J. RNA 2005, 11:1884-1897.
122. Olson W.K. Macromolecules 1975, 8:272-275.
123. Malhotra A., Gabb H.A., Harvey S.C. Curr. Opin. Struct. Biol. 1993, 3:241-246.
124. Malhotra A., Tan R.K.Z., Harvey S.C. Biophys. J. 1994, 66:1777-1795.
125. Kim N., Zahran M., Schlick T. Methods Enzymol. 2015, 553:115-135.
126. Kerpedjiev P., Honer Zu Siederdissen C., Hofacker I.L. RNA 2015, 21:1110-1121.
127. Jost D., Everaers R. J. Chem. Phys. 2010, 132:095101.
128. Hubbard J.M., Hearst J.E. Biochemistry 1991, 30:5458-5465.
129. Hubbard J.M., Hearst J.E. J. Mol. Biol. 1991, 221:889-907.
130. Malhotra A., Tan R.K.Z., Harvey S.C. J. Comput. Chem. 1994, 15:190-199.
131. Tan R.K., Petrov A.S., Harvey S.C. J. Chem. Theory Comput. 2006, 2:529-540.
132. Ding F., Tsao D., Nie H., Dokholyan N.V. Structure 2008, 16:1010-1018.
133. Gherghe C.M., Leonard C.W., Ding F., Dokholyan N.V., Weeks K.M. J. Am. Chem. Soc. 2009, 131:2541-2546.
134. Hyeon C., Thirumalai D. Proc. Natl. Acad. Sci. 2005, 102:6789-6794.
135. Mathews D.H., Sabina J., Zuker M., Turner D.H. J. Mol. Biol. 1999, 288:911-940.
136. Xia T., SantaLucia J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., Turner D.H. Biochemistry 1998, 37:14719-14735.
137. Xia Z., Gardner D.P., Gutell R.R., Ren P. J. Phys. Chem. B 2010, 114:13497-13506.
138. Xia Z., Bell D.R., Shi Y., Ren P. J. Phys. Chem. B 2013, 117:3135-3144.
139. Sharma S., Ding F., Dokholyan N.V. Bioinformatics 2008, 24:1951-1952.
140. Pincus D.L., Cho S.S., Hyeon C.B., Thirumalai D. Prog. Mol. Biol. Transl. 2008, 84:203.
141. Sippl M.J. J. Mol. Biol. 1990, 213:859-883.
142. Hamelryck T., Borg M., Paluszewski M., Paulsen J., Frellsen J., Andreetta C., Boomsma W., Bottaro S., Ferkinghoff-Borg J. PLoS One 2010, 5.
143. Taxilaga-Zetina O., Pliego-Pastrana P., Carbajal-Tinoco M.D. J. Chem. Phys. 2014, 140:115106.
144. Cao S., Chen S.J. J. Phys. Chem. B 2011, 115:4216-4226.
145. Cao S., Giedroc D.P., Chen S.J. RNA 2010, 16:538-552.
146. Xu X.J., Chen S.J. Biophys. Rep. 2015.
147. Mustoe A.M., Al-Hashimi H.M., Brooks C.L. J. Phys. Chem. B 2014, 118:2615-2627.
148. Denesyuk N.A., Thirumalai D. J. Phys. Chem. B 2013, 117:4901-4911.
149. Tan Z.J., Chen S.J. Biophys. J. 2007, 92:3615-3632.
150. Zhu Y., He Z., Chen S.J. PLoS One 2015, 10.
151. He Z., Zhu Y., Chen S.J. Phys. Chem. Chem. Phys. 2014, 16:6367-6375.
152. He Z., Chen S.J. J. Chem. Theory Comput. 2012, 8:2095-2101.
153. Bernauer J., Huang X., Sim A.Y., Levitt M. RNA 2011, 17:1066-1075.
154. Sim A.Y.L., Levitt M., Minary P. Proc. Natl. Acad. Sci. 2012, 109:2890-2895.
155. Brion P., Westhof E. Annu. Rev. Biophys. Biomol. Struct. 1997, 26:113-137.
156. Tinoco I., Bustamante C. J. Mol. Biol. 1999, 293:271-281.
157. Jaeger L., Westhof E., Leontis N.B. Nucleic Acids Res. 2001, 29:455-463.
158. Dawson W., Yamamoto K., Shimizu K., Kawai G. J. Nucleic Acids Invest. 2013, 4.
159. Geman S., Geman D. IEEE Trans. Pattern Anal. Mach. Intell. 1984, 6:721-741.
160. Hansmann U.H., Okamoto Y. Curr. Opin. Struct. Biol. 1999, 9:177-183.
161. Kirkpatrick S., Gelatt C.D., Vecchi M.P. Science 1983, 220:671-680.
162. Kumar S., Rosenberg J.M., Bouzida D., Swendsen R.H., Kollman P.A. J. Comput. Chem. 1995, 16:1339-1350.
163. Kumar S., Bouzida D., Swendsen R.H., Kollman P.A., Rosenberg J.M. J. Comput. Chem. 1992, 13:1011-1021.
164. Roux B. Comput. Phys. Commun. 1995, 91:275-278.
165. Sugita Y., Okamoto Y. Chem. Phys. Lett. 1999, 314:141-151.
166. Laio A., Parrinello M. Proc. Natl. Acad. Sci. 2002, 99:12562-12566.
167. Tesi M.C., Jans van Rensberg E.J., Orlandini E., Whittington S.G. J. Stat. Phys. 1996, 82:155-181.
168. Rhee Y.M., Pande V.S. Biophys. J. 2003, 84:775-786.
169. Whitelam S., Feng E.H., Hagan M.F., Geissler P.L. Soft Matter 2009, 5:1251-1262.
170. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., Teller E. J. Chem. Phys. 1953, 21:1087-1092.
171. Frellsen J., Moltke I., Thiim M., Mardia K.V., Ferkinghoff-Borg J., Hamelryck T. PLoS Comput. Biol. 2009, 5.
172. Ferrenberg A.M., Swendsen R.H. Phys. Rev. Lett. 1988, 61:2635-2638.
173. Ferrenberg A.M., Swendsen R.H. Phys. Rev. Lett. 1989, 63:1195-1198.
174. Nakajima N., Nakamura H., Kidera A. J. Phys. Chem. B 1997, 101:817-824.
175. Hansmann U.H.E., Okamoto Y., Eisenmenger F. Chem. Phys. Lett. 1996, 259:321-330.
176. Berg B.A., Neuhaus T. Phys. Rev. Lett. 1992, 68:9-12.
177. Janke W. Phys. A 1998, 254:164-178.
178. Glover F. Comput. Oper. Res. 1986, 13:533-549.
179. Harada R., Takano Y., Shigeta Y. J. Comput. Chem. 2015, 36:763-772.
180. Chekmarev S.F. Phys. Rev. E 2001, 64:036703.
181. Cvijovic D., Klinowski J. Science 1995, 267:664-666.
182. Harada R., Takano Y., Baba T., Shigeta Y. Phys. Chem. Chem. Phys. 2015, 17:6155-6173.
183. Sosnick T.R., Barrick D. Curr. Opin. Struct. Biol. 2011, 21:12-24.
184. Samudrala R., Moult J. J. Mol. Biol. 1998, 279:287-302.
185. Vassura M., Margara L., Fariselli P., Casadio R. Artif. Intell. Med. 2009, 45:229-237.
186. Harada R., Kitao A. J. Phys. Chem. B 2011, 115:8806-8812.
187. Serohijos A.W., Tsygankov D., Liu S., Elston T.C., Dokholyan N.V. Phys. Chem. Chem. Phys. 2009, 11:4840-4850.
188. Miao Z., Adamiak R.W., Blanchet M.F., Boniecki M., Bujnicki J.M., Chen S.J., Cheng C., Chojnowski G., Chou F.C., Cordero P., Cruz J.A., Ferre-D'Amare A.R., Das R., Ding F., Dokholyan N.V., Dunin-Horkawicz S., Kladwang W., Krokhotin A., Lach G., Magnus M., Major F., Mann T.H., Masquida B., Matelska D., Meyer M., Peselis A., Popenda M., Purzycka K.J., Serganov A., Stasiewicz J., Szachniuk M., Tandon A., Tian S., Wang J., Xiao Y., Xu X., Zhang J., Zhao P., Zok T., Westhof E. RNA 2015, 21:1066-1084.
189. Cruz J.A., Blanchet M.F., Boniecki M., Bujnicki J.M., Chen S.J., Cao S., Das R., Ding F., Dokholyan N.V., Flores S.C., Huang L., Lavender C.A., Lisi V., Major F., Mikolajczak K., Patel D.J., Philips A., Puton T., Santalucia J., Sijenyi F., Hermann T., Rother K., Rother M., Serganov A., Skorupski M., Soltysinski T., Sripakdeevong P., Tuszynska I., Weeks K.M., Waldsich C., Wildauer M., Leontis N.B., Westhof E. RNA 2012, 18:610-625.
190. Hajdin C.E., Ding F., Dokholyan N.V., Weeks K.M. RNA 2010, 16:1340-1349.
191. Kryshtafovych A., Moult J., Bales P., Bazan J.F., Biasini M., Burgin A., Chen C., Cochran F.V., Craig T.K., Das R., Fass D., Garcia-Doval C., Herzberg O., Lorimer D., Luecke H., Ma X., Nelson D.C., van Raaij M.J., Rohwer F., Segall A., Seguritan V., Zeth K., Schwede T. Proteins 2014, 82(Suppl. 2):26-42.
192. Moult J., Fidelis K., Kryshtafovych A., Schwede T., Tramontano A. Proteins 2014, 82(Suppl. 2):1-6.
193. Norambuena T., Cares J.F., Capriotti E., Melo F. Bioinformatics 2013, 29:2649-2650.
194. Pasquali S., Derreumaux P. J. Phys. Chem. B 1966, 114(2010):11957-11966.
195. Krokhotin A., Dokholyan N.V. Methods Enzymol. 2015, 553:65-89.
196. Jonikas M.A., Radmer R.J., Altman R.B. Bioinformatics 2009, 25:3259-3266.
197. Sykes M.T., Levitt M. J. Mol. Biol. 2005, 351:26-38.