-
1
-
-
0025315854
-
Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
-
Abrahams,J.P. et al. (1990) Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res. 18, 3035-3044.
-
(1990)
Nucleic Acids Res
, vol.18
, pp. 3035-3044
-
-
Abrahams, J.P.1
-
2
-
-
0041940818
-
Dynamic programming algorithms for RNA secondary structure prediction vhth pseudoknots
-
Akutsu,T (2000) Dynamic programming algorithms for RNA secondary structure prediction vhth pseudoknots. Discrete Appl. Math., 104, 45-62.
-
(2000)
Discrete Appl. Math
, vol.104
, pp. 45-62
-
-
Akutsu, T.1
-
3
-
-
0344298926
-
The Ribonuclease P Database
-
Brown,J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res., 27, 314.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 314
-
-
Brown, J.W.1
-
4
-
-
2442466703
-
Classifying RNA pseudoknotted structures
-
Condon,A. et al. (2004) Classifying RNA pseudoknotted structures. Theor. Comp. Sci., 320, 35-50.
-
(2004)
Theor. Comp. Sci
, vol.320
, pp. 35-50
-
-
Condon, A.1
-
5
-
-
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. Comput. Chem., 24, 1664-1677.
-
(2003)
J. Comput. Chem
, vol.24
, pp. 1664-1677
-
-
Dirks, R.M.1
Pierce, N.A.2
-
6
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy,S.R. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
7
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier,S.M. et al. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA, 93, 9373-9377.
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 9373-9377
-
-
Freier, S.M.1
-
8
-
-
0029061125
-
The computer simulation of RNA folding pathways using a genetic algorithm
-
Gultyaev,A.P. et al. (1995) The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250, 37-51.
-
(1995)
J. Mol. Biol
, vol.250
, pp. 37-51
-
-
Gultyaev, A.P.1
-
9
-
-
0034522921
-
RNA secondary structure: Physical and computational aspects
-
Higgs,P.G. (2000) RNA secondary structure: Physical and computational aspects. Q. Rev. Biophys., 33, 199-253.
-
(2000)
Q. Rev. Biophys
, vol.33
, pp. 199-253
-
-
Higgs, P.G.1
-
10
-
-
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
-
11
-
-
33846900179
-
High sensitivity RNA pseudoknot prediction
-
Huang,X. and Ali,H. (2007) High sensitivity RNA pseudoknot prediction. Nucleic Acids Res., 35, 656-663.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 656-663
-
-
Huang, X.1
Ali, H.2
-
12
-
-
0034612331
-
Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme
-
Isambert,H. and Siggia,E.D. (2000) Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme. Proc. Natl Acad. Sci. USA, 97, 6515-6520.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 6515-6520
-
-
Isambert, H.1
Siggia, E.D.2
-
13
-
-
24044475960
-
-
Addison-Wesley Longman Publishing Co, Inc, USA
-
Kleinberg,J. and Tardos,E. (2005) Algorithm Design. Addison-Wesley Longman Publishing Co., Inc., USA.
-
(2005)
Algorithm Design
-
-
Kleinberg, J.1
Tardos, E.2
-
14
-
-
0032796501
-
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
-
Knudsen,B. and Hein,J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioiformatics, 15, 446-454.
-
(1999)
Bioiformatics
, vol.15
, pp. 446-454
-
-
Knudsen, B.1
Hein, J.2
-
15
-
-
0033709625
-
RNA pseudoknot prediction in energy-based models
-
Lyngso,R.B. and Pedersen,C.N. (2000) RNA pseudoknot prediction in energy-based models. J. Comput. Biol., 7, 409-427.
-
(2000)
J. Comput. Biol
, vol.7
, pp. 409-427
-
-
Lyngso, R.B.1
Pedersen, C.N.2
-
16
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H. et al. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
-
(1999)
J. Mol. Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
-
17
-
-
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
-
18
-
-
25844447772
-
HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
-
Ren,J. et al. (2005) HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11, 1494-1504.
-
(2005)
RNA
, vol.11
, pp. 1494-1504
-
-
Ren, J.1
-
19
-
-
0033524952
-
-
Rivas,E. and Eddy.S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285 2053-2068.
-
Rivas,E. and Eddy.S.R. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285 2053-2068.
-
-
-
-
20
-
-
0347724163
-
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
-
Ruan,J. et al. (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.1
-
22
-
-
0029100233
-
Predicting thermodynamic properties of RNA
-
Serra,M.J. and Turner,D.H. (1995) Predicting thermodynamic properties of RNA. Methods Enzymol., 259, 242-261.
-
(1995)
Methods Enzymol
, vol.259
, pp. 242-261
-
-
Serra, M.J.1
Turner, D.H.2
-
23
-
-
0031804156
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl,M. et al. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res., 26, 148-153.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 148-153
-
-
Sprinzl, M.1
-
24
-
-
0036084598
-
5S Ribosomal RNA Database
-
Szymanski,M. et al. (2002) 5S Ribosomal RNA Database. Nucleic Acids Res., 30, 176-178.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 176-178
-
-
Szymanski, M.1
-
25
-
-
0033954144
-
PseudoBase: A database with RNA pseudoknots
-
van Batenburg,F.H. et al. (2000) PseudoBase: A database with RNA pseudoknots. Nucleic Acids Res., 28, 201-204.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 201-204
-
-
van Batenburg, F.H.1
-
26
-
-
0028000994
-
Coaxial stacking of helixes enhances of binding of oligoribonucleotides and improves predictions of RNA folding
-
Walter,A.E. et al. (1994) Coaxial stacking of helixes enhances of binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad. Sci. USA, 91, 9218-9222.
-
(1994)
Proc Natl Acad. Sci. USA
, vol.91
, pp. 9218-9222
-
-
Walter, A.E.1
-
27
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker,M. and Stiegler,P. (1991) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
-
(1991)
Nucleic Acids Res
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|