-
1
-
-
0041940818
-
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
-
Akutsu, T.: Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl. Math. 104(1-3), 45-62 (2000)
-
(2000)
Discrete Appl. Math.
, vol.104
, Issue.1-3
, pp. 45-62
-
-
Akutsu, T.1
-
2
-
-
34547840261
-
Efficient parameter estimation for RNA secondary structure prediction
-
Andronescu, M.S., Condon, A.E., Hoos, H.H., Mathews, D.H., Murphy, K.P.: Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 23, 19-28 (2007)
-
(2007)
Bioinformatics
, vol.23
, pp. 19-28
-
-
Andronescu, M.S.1
Condon, A.E.2
Hoos, H.H.3
Mathews, D.H.4
Murphy, K.P.5
-
3
-
-
75649099055
-
Improved free energy parameters for RNA pseudoknotted secondary structure prediction
-
Andronescu, M.S., Pop, C., Condon, A.E.: Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA 16(1), 26-42 (2010)
-
(2010)
RNA
, vol.16
, Issue.1
, pp. 26-42
-
-
Andronescu, M.S.1
Pop, C.2
Condon, A.E.3
-
4
-
-
27544437866
-
Structure clustering features on the Sfold Web server
-
Chan, C.Y., Lawrence, C.E., Ding, Y.: Structure clustering features on the Sfold Web server. Bioinformatics 21(20), 3926-3928 (2005)
-
(2005)
Bioinformatics
, vol.21
, Issue.20
, pp. 3926-3928
-
-
Chan, C.Y.1
Lawrence, C.E.2
Ding, Y.3
-
5
-
-
0028168585
-
Characterization of a kissing hairpin complex derived from the human immunodeficiency virus genome
-
Chang, K.Y., Tinoco, I.: Characterization of a kissing hairpin complex derived from the human immunodeficiency virus genome. Proc. Natl. Acad. Sci. USA 91(18), 8705-8709 (1994)
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, Issue.18
, pp. 8705-8709
-
-
Chang, K.Y.1
Tinoco, I.2
-
6
-
-
69249214078
-
5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids
-
5) Algorithm for MFE Prediction of Kissing Hairpins and 4-Chains in Nucleic Acids. J. Comput. Biol. 16(6), 803-815 (2009)
-
(2009)
J. Comput. Biol.
, vol.16
, Issue.6
, pp. 803-815
-
-
Chen, H.L.1
Condon, A.E.2
Jabbari, H.3
-
7
-
-
58249131021
-
Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges
-
Condon, A.E., Jabbari, H.: Computational prediction of nucleic acid secondary structure: Methods, applications, and challenges. Theoretical Computer Science 410(4-5), 294-301 (2009)
-
(2009)
Theoretical Computer Science
, vol.410
, Issue.4-5
, pp. 294-301
-
-
Condon, A.E.1
Jabbari, H.2
-
8
-
-
70350398439
-
PMFastR: A New Approach to Multiple RNA Structure Alignment
-
Salzberg, S.L., Warnow, T. (eds.) WABI 2009. Springer, Heidelberg
-
Deblasio, D., Bruand, J., Zhang, S.: PMFastR: A New Approach to Multiple RNA Structure Alignment. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 49-61. Springer, Heidelberg (2009)
-
(2009)
LNCS
, vol.5724
, pp. 49-61
-
-
Deblasio, D.1
Bruand, J.2
Zhang, S.3
-
9
-
-
76949088582
-
3/ log n)-time Algorithm for RNA folding using the Four-Russians Speedup
-
3/ log n)-time Algorithm for RNA folding using the Four-Russians Speedup. Algorithms Mol. Biol. 5(1), 13 (2010)
-
(2010)
Algorithms Mol. Biol.
, vol.5
, Issue.1
, pp. 13
-
-
Frid, Y.1
Gusfield, D.2
-
10
-
-
84937404651
-
Explaining and Controlling Ambiguity in Dynamic Programming
-
Giancarlo, R., Sankoff, D. (eds.) CPM 2000. Springer, Heidelberg
-
Giegerich, R.: Explaining and Controlling Ambiguity in Dynamic Programming. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 46-59. Springer, Heidelberg (2000)
-
(2000)
LNCS
, vol.1848
, pp. 46-59
-
-
Giegerich, R.1
-
12
-
-
2442604484
-
A discipline of dynamic programming over sequence data
-
Giegerich, R., Meyer, C., Steffen, P.: A discipline of dynamic programming over sequence data. Science of Computer Programming 51(3), 215-263 (2004)
-
(2004)
Science of Computer Programming
, vol.51
, Issue.3
, pp. 215-263
-
-
Giegerich, R.1
Meyer, C.2
Steffen, P.3
-
13
-
-
0027722243
-
An 'elaborated' pseudoknot is required for high frequency frameshifting during translation of HCV 229E polymerase mRNA
-
Herold, J., Siddell, S.G.: An 'elaborated' pseudoknot is required for high frequency frameshifting during translation of HCV 229E polymerase mRNA. Nucl. Acids Res. 21(25), 5838-5842 (1993)
-
(1993)
Nucl. Acids Res.
, vol.21
, Issue.25
, pp. 5838-5842
-
-
Herold, J.1
Siddell, S.G.2
-
14
-
-
34249772381
-
Fast Folding and Comparison of RNA Secondary Structures
-
Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S.L., Tacker, M., Schuster, P.: Fast Folding and Comparison of RNA Secondary Structures. Monatsh. Chem. 125, 167-188 (1994)
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, S.L.4
Tacker, M.5
Schuster, P.6
-
15
-
-
33750447980
-
Unusual mechanical stability of a minimal RNA kissing complex
-
Li, P.T.X., Bustamante, C., Tinoco, I.: Unusual mechanical stability of a minimal RNA kissing complex. Proc. Natl. Acad. Sci. USA 103(43), 15847-15852 (2006)
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, Issue.43
, pp. 15847-15852
-
-
Li, P.T.X.1
Bustamante, C.2
Tinoco, I.3
-
16
-
-
0033709625
-
RNA Pseudoknot Prediction in Energy-Based Models
-
Lyngsø, R.B., Pedersen, C.N.S.: RNA Pseudoknot Prediction in Energy-Based Models. J. Comput. Biol. 7(3-4), 409-427 (2000)
-
(2000)
J. Comput. Biol.
, vol.7
, Issue.3-4
, pp. 409-427
-
-
Lyngsø, R.B.1
Pedersen, C.N.S.2
-
17
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M., Turner, D.H.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101(19), 7287-7292 (2004)
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.19
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
18
-
-
33744790273
-
Prediction of RNA secondary structure by free energy minimization
-
Mathews, D.H., Turner, D.H.: Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol. 16(3), 270-278 (2006)
-
(2006)
Curr. Opin. Struct. Biol.
, vol.16
, Issue.3
, pp. 270-278
-
-
Mathews, D.H.1
Turner, D.H.2
-
19
-
-
0031060472
-
Kissing of the two predominant hairpin loops in the coxsackie B virus 3′ untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis
-
Melchers, W.J.G., Hoenderop, J.G.J., Slot, H.J.B., Pleij, C.W.A., Pilipenko, E.V., Agol, V.I., Galama, J.M.D.: Kissing of the two predominant hairpin loops in the coxsackie B virus 3′ untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis. J. Virol. 71(1), 686-696 (1997)
-
(1997)
J. Virol.
, vol.71
, Issue.1
, pp. 686-696
-
-
Melchers, W.J.G.1
Hoenderop, J.G.J.2
Slot, H.J.B.3
Pleij, C.W.A.4
Pilipenko, E.V.5
Agol, V.I.6
Galama, J.M.D.7
-
20
-
-
13244252326
-
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
-
DOI 10.1186/1471-2105-5-104
-
Reeder, J., Giegerich, R.: Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5(1), 104 (2004) (Pubitemid 40195401)
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 104
-
-
Reeder, J.1
Giegerich, R.2
-
21
-
-
25844447772
-
HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
-
Ren, J., Rastegari, B., Condon, A.E., Hoos, H.H.: HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA 11(10), 1494-1504 (2005)
-
(2005)
RNA
, vol.11
, Issue.10
, pp. 1494-1504
-
-
Ren, J.1
Rastegari, B.2
Condon, A.E.3
Hoos, H.H.4
-
22
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas, E., Eddy, S.R.: A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol. 285(5), 2053-2068 (1999)
-
(1999)
J. Mol. Biol.
, vol.285
, Issue.5
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
23
-
-
33749252538
-
Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence
-
Rødland, E.A.: Pseudoknots in RNA Secondary Structures: Representation, Enumeration, and Prevalence. J. Comput. Biol. 13(6), 1197-1213 (2006)
-
(2006)
J. Comput. Biol.
, vol.13
, Issue.6
, pp. 1197-1213
-
-
Rødland, E.A.1
-
24
-
-
0026651981
-
RNA pseudoknots that inhibit HIV type 1 reverse transcriptase
-
Tuerk, C., MacDougal, S., Gold, L.: RNA pseudoknots that inhibit HIV type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA 89(15), 6988-6992 (1992)
-
(1992)
Proc. Natl. Acad. Sci. USA
, vol.89
, Issue.15
, pp. 6988-6992
-
-
Tuerk, C.1
MacDougal, S.2
Gold, L.3
-
25
-
-
0035170790
-
PseudoBase: Structural information on RNA pseudoknots
-
van Batenburg, F.H.D., Gultyaev, A.P., Pleij, C.W.A.: PseudoBase: structural information on RNA pseudoknots. Nucl. Acids Res. 29(1), 194-195 (2001)
-
(2001)
Nucl. Acids Res.
, vol.29
, Issue.1
, pp. 194-195
-
-
Van Batenburg, F.H.D.1
Gultyaev, A.P.2
Pleij, C.W.A.3
-
26
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
DOI 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G
-
Wuchty, S., Fontana, W., Hofacker, I.L., Schuster, P.: Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49(2), 145-165 (1999) (Pubitemid 29061655)
-
(1999)
Biopolymers
, vol.49
, Issue.2
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
27
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9(1), 133-148 (1981)
-
(1981)
Nucl. Acids Res.
, vol.9
, Issue.1
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|