-
1
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker,M. and Stiegler,P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
2
-
-
13444292041
-
An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model
-
Clote,P. (2005) An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J. Comput. Biol., 12, 83-101.
-
(2005)
J. Comput. Biol.
, vol.12
, pp. 83-101
-
-
Clote, P.1
-
3
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker,M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
4
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker,I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
5
-
-
0026483177
-
Structural and functional aspects of RNA pseudoknots
-
Dam,E., Pleij,K. and Draper,D. (1992) Structural and functional aspects of RNA pseudoknots. Biochemistry, 31, 11665-11676.
-
(1992)
Biochemistry
, vol.31
, pp. 11665-11676
-
-
Dam, E.1
Pleij, K.2
Draper, D.3
-
6
-
-
0033954144
-
PseudoBase: A database with RNA pseudoknots
-
Batenburg,F., Gultyaev,A.P., Pleij,C., Ng,J. and Oliehoek,J. (2000) PseudoBase: A database with RNA pseudoknots. Nucleic Acids Res., 28, 201-204.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 201-204
-
-
Batenburg, F.1
Gultyaev, A.P.2
Pleij, C.3
Ng, J.4
Oliehoek, J.5
-
7
-
-
0029331431
-
An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region
-
Wang,C., Le,S.Y., Ali,N. and Siddiqui,A. (1995) An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region. RNA, 1, 526-537.
-
(1995)
RNA
, vol.1
, pp. 526-537
-
-
Wang, C.1
Le, S.Y.2
Ali, N.3
Siddiqui, A.4
-
8
-
-
0029896020
-
Recoding: Dynamic reprogramming of translation
-
Gesteland,R.F. and Atkins,J.F. (1996) Recoding: Dynamic reprogramming of translation. Annu. Rev. Biochem., 65, 741-768.
-
(1996)
Annu. Rev. Biochem.
, vol.65
, pp. 741-768
-
-
Gesteland, R.F.1
Atkins, J.F.2
-
9
-
-
0033532081
-
Evidence for an RNA pseudoknot loop-helix interaction essential for efficient-1 ribosomal frameshifting
-
Liphardt,J., Napthine,S., Kontos,H. and Brierley,I. (1999) Evidence for an RNA pseudoknot loop-helix interaction essential for efficient-1 ribosomal frameshifting. J. Mol. Biol., 288, 321-335.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 321-335
-
-
Liphardt, J.1
Napthine, S.2
Kontos, H.3
Brierley, I.4
-
10
-
-
17844384225
-
Torsional restraint: A new twist on frameshifting pseudoknots
-
Plant,E.P. and Dinman,J.D. (2005) Torsional restraint: A new twist on frameshifting pseudoknots. Nucleic Acids Res., 33, 1825-1833.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 1825-1833
-
-
Plant, E.P.1
Dinman, J.D.2
-
11
-
-
0037316485
-
The 9-A solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting
-
Plant,E.P., Jacobs,K.L., Harger,J.W., Meskauskas,A., Jacobs,J.L., Baxter,J.L., Petrov,A.N. and Dinman,J.D. (2003) The 9-A solution: How mRNA pseudoknots promote efficient programmed -1 ribosomal frameshifting. RNA, 9, 168-174.
-
(2003)
RNA
, vol.9
, pp. 168-174
-
-
Plant, E.P.1
Jacobs, K.L.2
Harger, J.W.3
Meskauskas, A.4
Jacobs, J.L.5
Baxter, J.L.6
Petrov, A.N.7
Dinman, J.D.8
-
12
-
-
0033010932
-
Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot
-
Su,L., Chen,L., Egli,M., Berger,J.M. and Rich,A. (1999) Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot. Nature Struct. Biol., 6, 285-292.
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 285-292
-
-
Su, L.1
Chen, L.2
Egli, M.3
Berger, J.M.4
Rich, A.5
-
13
-
-
0033452721
-
Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency
-
Kim,Y.G., Su,L., Maas,S., O'Neill,A. and Rich,A. (1999) Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency. Proc. Natl Acad. Sci. USA, 96, 14234-14239.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 14234-14239
-
-
Kim, Y.G.1
Su, L.2
Maas, S.3
O'Neill, A.4
Rich, A.5
-
14
-
-
24644473489
-
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting
-
Cornish,P.V., Hennig,M. and Giedroc,D.P. (2005) A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting. Proc. Natl Acad. Sci. USA, 102, 12694-12699.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 12694-12699
-
-
Cornish, P.V.1
Hennig, M.2
Giedroc, D.P.3
-
15
-
-
16244365573
-
Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita
-
Yingling,Y.G. and Shapiro,B.A. (2005) Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita. J. Mol. Biol., 348, 27-42.
-
(2005)
J. Mol. Biol.
, vol.348
, pp. 27-42
-
-
Yingling, Y.G.1
Shapiro, B.A.2
-
16
-
-
0031730497
-
An RNA folding method capable of identifying pseudoknots and base triples
-
Tabaska,J.E., Cary,R.B., Gabow,H.N. and Stormo,G.D. (1998) An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14, 691-699.
-
(1998)
Bioinformatics
, vol.14
, pp. 691-699
-
-
Tabaska, J.E.1
Cary, R.B.2
Gabow, H.N.3
Stormo, G.D.4
-
17
-
-
0026466830
-
Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods
-
Gutell,R.R., Power,A., Hertz,G.Z., Putz,E.J. and Stormo,G.D. (1992) Identifying constraints on the higher-order structure of RNA: Continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-5795.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 5785-5795
-
-
Gutell, R.R.1
Power, A.2
Hertz, G.Z.3
Putz, E.J.4
Stormo, G.D.5
-
18
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas,E. and Eddy,S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.R.2
-
19
-
-
0043285072
-
A partition function algorithm for nucleic acid secondary structure including pseudoknots
-
Dirks,R.M. and Pierce,N.A. (2003) A partition function algorithm for nucleic acid secondary structure including pseudoknots. J. Comp. Chem., 24, 1664-1677.
-
(2003)
J. Comp. Chem.
, vol.24
, pp. 1664-1677
-
-
Dirks, R.M.1
Pierce, N.A.2
-
20
-
-
13244252326
-
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
-
Reeder,J. and Giegerich,R. (2004) Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics, 5, 104.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 104
-
-
Reeder, J.1
Giegerich, R.2
-
21
-
-
0347724163
-
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
-
Ruan,J.R., Stormo,G.D. and Zhang,W. (2004) An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots. Bioinformatics, 20, 58-66.
-
(2004)
Bioinformatics
, vol.20
, pp. 58-66
-
-
Ruan, J.R.1
Stormo, G.D.2
Zhang, W.3
-
22
-
-
25844447772
-
HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
-
Ren,J., Rastegari,B., Condon,A. and Hoos,H.H. (2005) HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11, 1494-1504.
-
(2005)
RNA
, vol.11
, pp. 1494-1504
-
-
Ren, J.1
Rastegari, B.2
Condon, A.3
Hoos, H.H.4
-
23
-
-
0027932176
-
Thermodynamics of folding a pseudoknotted mRNA fragment
-
Gluick,T.C. and Draper,D.E. (1994) Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol., 241, 246-326.
-
(1994)
J. Mol. Biol.
, vol.241
, pp. 246-326
-
-
Gluick, T.C.1
Draper, D.E.2
-
24
-
-
0032948718
-
An approximation of loop free energy values of RNA H-pseudoknots
-
Gultyaev,A.P., Batenburg,F. and Pleij,C. (1999) An approximation of loop free energy values of RNA H-pseudoknots. RNA, 5, 609-617.
-
(1999)
RNA
, vol.5
, pp. 609-617
-
-
Gultyaev, A.P.1
Batenburg, F.2
Pleij, C.3
-
25
-
-
17844378705
-
Asymmetry in RNA pseudoknots: Observation and theory
-
Aalberts,D.P. and Hodas,N.O. (2005) Asymmetry in RNA pseudoknots: observation and theory. Nucleic Acids Res., 33, 2210-2214.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2210-2214
-
-
Aalberts, D.P.1
Hodas, N.O.2
-
26
-
-
33744547883
-
Predicting RNA pseudoknot folding thermodynamics
-
Cao,S. and Chen,S.J. (2006) Predicting RNA pseudoknot folding thermodynamics. Nucleic Acids Res., 34, 2634-2652.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 2634-2652
-
-
Cao, S.1
Chen, S.J.2
-
28
-
-
33751175173
-
Protein motif searching through similar enriched parikh vector identification
-
Huang,X., Ali,H., Sadanandam,A. and Singh,R. (2005) Protein motif searching through similar enriched parikh vector identification. The fifth IEEE Symposium on BioInformatics and BioEngineering. pp. 285-289.
-
(2005)
The Fifth IEEE Symposium on BioInformatics and BioEngineering
, pp. 285-289
-
-
Huang, X.1
Ali, H.2
Sadanandam, A.3
Singh, R.4
-
29
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequences of two proteins
-
Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol., 48, 443-453.
-
(1970)
J. Mol. Biol.
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
30
-
-
0026651981
-
RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
-
Tuerk,C., MacDougal,S. and Gold,L. (1992) RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc. Natl Acad. Sci. USA, 89, 6988-6992.
-
(1992)
Proc. Natl Acad. Sci. USA
, vol.89
, pp. 6988-6992
-
-
Tuerk, C.1
MacDougal, S.2
Gold, L.3
-
31
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia,T., SantaLucia,J., Jr, Burkard,M.E., Kierzek,R., Schroeder,S.J., Jiao,X., Cox,C. and Turner,D.H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry, 37, 14719-14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
SantaLucia Jr., J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
Cox, C.7
Turner, D.H.8
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