-
1
-
-
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
-
2
-
-
0025315854
-
Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
-
Abrahams, J.P., van den Berg, M., van Batenburg, E., 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
van den Berg, M.2
van Batenburg, E.3
-
3
-
-
0041940818
-
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots
-
Akutsu, T. 2000. Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots. Discrete Appl. Math. 104, 45-62.
-
(2000)
Discrete Appl. Math
, vol.104
, pp. 45-62
-
-
Akutsu, T.1
-
4
-
-
0033428888
-
Programmed ribosomal frameshifting: Much ado about knotting!
-
Alam, S.L., Atkins, J.F., and Gesteland, R.F. 1999. Programmed ribosomal frameshifting: much ado about knotting! Proc. Natl. Acad. Sci. USA 96, 14177-14179.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 14177-14179
-
-
Alam, S.L.1
Atkins, J.F.2
Gesteland, R.F.3
-
5
-
-
0034767147
-
A linear-time algorithm for computing inversion distance between signed permutations with an experimental study
-
Bader, D.A., Moret, B.M.E., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 483-491.
-
(2001)
J. Comput. Biol
, vol.8
, pp. 483-491
-
-
Bader, D.A.1
Moret, B.M.E.2
Yan, M.3
-
6
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., et al. 2000. The protein data bank. Nucleic Acids Res. 28, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
-
7
-
-
11144330098
-
Natural and engineered nucleic acids as tools to explore biology
-
Breaker, R.R. 2004. Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838-845.
-
(2004)
Nature
, vol.432
, pp. 838-845
-
-
Breaker, R.R.1
-
8
-
-
2942571539
-
-
Cannone, J.J., Subramanian, S., Schnare, M.N., et al. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformtics 3.
-
Cannone, J.J., Subramanian, S., Schnare, M.N., et al. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformtics 3.
-
-
-
-
9
-
-
2442466703
-
Classifying RNA pseudoknotted structures
-
Condon, A., Davy, B., Rastegari, B., et al. 2004. Classifying RNA pseudoknotted structures. Theor. Comput. Sci. 320, 35-50.
-
(2004)
Theor. Comput. Sci
, vol.320
, pp. 35-50
-
-
Condon, A.1
Davy, B.2
Rastegari, B.3
-
10
-
-
0022422660
-
Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984
-
Cornish-Bowden, A. 1985. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. 13, 3021-3030.
-
(1985)
Nucleic Acids Res
, vol.13
, pp. 3021-3030
-
-
Cornish-Bowden, A.1
-
11
-
-
0031428303
-
Pseudoknots: A vital feature in viral RNA
-
Deiman, B.A., and Pleij, C.W. 1997. Pseudoknots: a vital feature in viral RNA. Semin. Virol. 8, 166-175.
-
(1997)
Semin. Virol
, vol.8
, pp. 166-175
-
-
Deiman, B.A.1
Pleij, C.W.2
-
12
-
-
0037062973
-
The brave new world of RNA
-
Dennis, C. 2002. The brave new world of RNA. Nature 418, 122-124.
-
(2002)
Nature
, vol.418
, pp. 122-124
-
-
Dennis, C.1
-
13
-
-
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
-
14
-
-
0036240768
-
Deoxyribozymes: New activities and new applications
-
Emilsson, G.M., and Breaker, R.R. 2002. Deoxyribozymes: new activities and new applications. Cell. Mol. Life Sci. 59, 596-607.
-
(2002)
Cell. Mol. Life Sci
, vol.59
, pp. 596-607
-
-
Emilsson, G.M.1
Breaker, R.R.2
-
15
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
Ferré-D'Amaré, A.R., Zhou, K., and Doudna, J.A. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574.
-
(1998)
Nature
, vol.395
, pp. 567-574
-
-
Ferré-D'Amaré, A.R.1
Zhou, K.2
Doudna, J.A.3
-
16
-
-
0031577194
-
Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot
-
Gluick, T.C., Gerstner, R.B., and Draper, D.E. 1997. Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot. J. Mol. Biol. 270, 451-463.
-
(1997)
J. Mol. Biol
, vol.270
, pp. 451-463
-
-
Gluick, T.C.1
Gerstner, R.B.2
Draper, D.E.3
-
17
-
-
0029061125
-
The computer simulation of RNA folding pathways using a genetic algorithm
-
Gultyaev, A.P., van Batenburg, F.H., and Pleij, C.W. 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
van Batenburg, F.H.2
Pleij, C.W.3
-
18
-
-
0041620358
-
Pseudoviewer2: Visualization of RNA pseudoknots of any type
-
Han, K., and Byun, Y. 2003. Pseudoviewer2: visualization of RNA pseudoknots of any type. Nucleic Acids Res. 31, 3432-3440.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3432-3440
-
-
Han, K.1
Byun, Y.2
-
19
-
-
3042732096
-
Directed evolution of nucleic acid enzymes
-
Joyce, G.F. 2004. Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73, 791-836.
-
(2004)
Annu. Rev. Biochem
, vol.73
, pp. 791-836
-
-
Joyce, G.F.1
-
20
-
-
0032540504
-
NMR structure of a classical pseudoknot: Interplay of single-and double-stranded RNA
-
Kolk, M.H., van der Graaf, M., Wijmenga, S.S., et al. 1998. NMR structure of a classical pseudoknot: interplay of single-and double-stranded RNA. Science 280, 434-438.
-
(1998)
Science
, vol.280
, pp. 434-438
-
-
Kolk, M.H.1
van der Graaf, M.2
Wijmenga, S.S.3
-
21
-
-
34047199201
-
Complexity of pseudoknot prediction in simple models
-
Lyngso, R.B. 2004: Complexity of pseudoknot prediction in simple models. Notes Comput. Sci. 3142, 919-931.
-
(2004)
Notes Comput. Sci
, vol.3142
, pp. 919-931
-
-
Lyngso, R.B.1
-
22
-
-
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
-
23
-
-
0032787871
-
Fast evaluation of internal loops in RNA secondary structure prediction
-
Lyngso, R., Zuker, M., and Pedersen, C. 1999. Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics 15, 440-445.
-
(1999)
Bioinformatics
, vol.15
, pp. 440-445
-
-
Lyngso, R.1
Zuker, M.2
Pedersen, C.3
-
24
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews, D.H., Sabina, J., Zuker, M., 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
Sabina, J.2
Zuker, M.3
-
25
-
-
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., Hoenderop, J.G., Pleij, C.W., et al. 1997. 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, 686-696.
-
(1997)
J. Virol
, vol.71
, pp. 686-696
-
-
Melchers, W.J.1
Hoenderop, J.G.2
Pleij, C.W.3
-
26
-
-
0019082587
-
Fast algorithm for predicting the secondary structure of single-stranded RNA
-
Nussinov, R., and Jacobson, A.B. 1980. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl. Acad. Sci. USA 77, 6309-6313.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 6309-6313
-
-
Nussinov, R.1
Jacobson, A.B.2
-
28
-
-
13244252326
-
-
Reeder, J., and Giegerich, R. 2004. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5.
-
Reeder, J., and Giegerich, R. 2004. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 5.
-
-
-
-
29
-
-
25844447772
-
Hotknots: Heuristic prediction of RNA secondary structures including pseudoknots
-
Ren, J., Rastegari, B., Condon, A., 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
Rastegari, B.2
Condon, A.3
-
30
-
-
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
-
31
-
-
14044251445
-
Algorithmic self-assembly of DNA Sierpinski triangles
-
Rothemund, P.W., Papadakis, N.P., and Winfree, E. 2004. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, 2041-2053.
-
(2004)
PLoS Biol
, vol.2
, pp. 2041-2053
-
-
Rothemund, P.W.1
Papadakis, N.P.2
Winfree, E.3
-
32
-
-
0031804028
-
DNA nanotechnology: Novel DNA construction
-
Seeman, N.C. 1998. DNA nanotechnology: novel DNA construction. Annu. Rev. Biophys. Biomol. Struct. 27, 225-248.
-
(1998)
Annu. Rev. Biophys. Biomol. Struct
, vol.27
, pp. 225-248
-
-
Seeman, N.C.1
-
33
-
-
24644464003
-
DNA nanodevices
-
Simmel, P.C., and Dittmer, W.U. 2005. DNA nanodevices. Small 1, 284-299.
-
(2005)
Small
, vol.1
, pp. 284-299
-
-
Simmel, P.C.1
Dittmer, W.U.2
-
34
-
-
13444288185
-
-
Sprinzl, M., and Vassilenko, K.S. 2005. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 33.
-
Sprinzl, M., and Vassilenko, K.S. 2005. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 33.
-
-
-
-
35
-
-
22744455135
-
Pseudoknots: RNA structures with diverse functions
-
Staple, D.W., and Butcher, S.E. 2005. Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3, 956-959.
-
(2005)
PLoS Biol
, vol.3
, pp. 956-959
-
-
Staple, D.W.1
Butcher, S.E.2
-
36
-
-
0001396964
-
Tree adjoining grammars for RNA structure prediction
-
Uemura, Y, Hasegawa, A., Kobayashi, S., et al. 1999. Tree adjoining grammars for RNA structure prediction. Theoret. Comput. Sci. 210, 277-303.
-
(1999)
Theoret. Comput. Sci
, vol.210
, pp. 277-303
-
-
Uemura, Y.1
Hasegawa, A.2
Kobayashi, S.3
-
37
-
-
0035170790
-
Pseudobase: Structural information of RNA pseudoknots
-
van Batenburg, F.H., Gultyaev, A.P., and Pleij, C.W. 2001. Pseudobase: structural information of RNA pseudoknots. Nucleic Acids Res. 29, 194-195.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 194-195
-
-
van Batenburg, F.H.1
Gultyaev, A.P.2
Pleij, C.W.3
-
38
-
-
0347364655
-
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
-
Xayaphoummine, A., Bucher, T., Thalmann, F., et al. 2003. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl Acad. Sci. USA 100, 15310-15315.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 15310-15315
-
-
Xayaphoummine, A.1
Bucher, T.2
Thalmann, F.3
-
39
-
-
0141534348
-
Dna-templated self-assembly of protein arrays and highly conductive nanowires
-
Yan, H., Park, S.H., Finkelstein, G., et al. 2003. Dna-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882-1884.
-
(2003)
Science
, vol.301
, pp. 1882-1884
-
-
Yan, H.1
Park, S.H.2
Finkelstein, G.3
-
41
-
-
0037246703
-
TMRDB (tmRNA database)
-
Zwieb, C., Gorodkin, J., Knudsen, B., et al. 2003. TMRDB (tmRNA database). Nucleic Acids Res. 31, 446-447.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 446-447
-
-
Zwieb, C.1
Gorodkin, J.2
Knudsen, B.3
|