-
1
-
-
33750214512
-
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
-
Lu, Z. J., Turner, D. H., and Mathews, D. H. (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation, Nucleic Acids Res. 34, 4912-4924.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4912-4924
-
-
Lu, Z.J.1
Turner, D.H.2
Mathews, D.H.3
-
2
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (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
Turner, D.H.4
-
3
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews, D. H., Disney, M. D., Childs, J. C., Schroeder, S. J., Zuker, M., and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proc. Natl. Acad. Sci. U.S.A. 101, 7287-7292.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A
, vol.101
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.C.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
4
-
-
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
-
5
-
-
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
-
6
-
-
33744825518
-
Predicting RNA Secondary Structure
-
3rd ed, Gesteland, R. F, Cech, T. R, and Atkins, J. F, Eds, pp, Cold Spring Harbor Laboratory Press, Cold Spring Harbor
-
Mathews, D. H., Schroeder, S. J., Turner, D. H., and Zuker, M. (2005). Predicting RNA Secondary Structure, in The RNA World, 3rd ed. (Gesteland, R. F., Cech, T. R., and Atkins, J. F., Eds.) pp 631-657, Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
-
(2005)
The RNA World
, pp. 631-657
-
-
Mathews, D.H.1
Schroeder, S.J.2
Turner, D.H.3
Zuker, M.4
-
7
-
-
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
-
8
-
-
1842388479
-
RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide
-
Recht, M. I., Fourmy, D., Blanchard, S. C., Dahlquist, K. D., and Puglisi, J. D. (1996) RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide, J. Mol. Biol. 262, 421-436.
-
(1996)
J. Mol. Biol
, vol.262
, pp. 421-436
-
-
Recht, M.I.1
Fourmy, D.2
Blanchard, S.C.3
Dahlquist, K.D.4
Puglisi, J.D.5
-
9
-
-
0030299990
-
G-A and U-U mismatches can stabilize RNA internal loops of three nucleotides
-
Schroeder, S., Kim, J., and Turner, D. H. (1996) G-A and U-U mismatches can stabilize RNA internal loops of three nucleotides, Biochemistry 35, 16105-16109.
-
(1996)
Biochemistry
, vol.35
, pp. 16105-16109
-
-
Schroeder, S.1
Kim, J.2
Turner, D.H.3
-
10
-
-
0034622514
-
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA
-
Schroeder, S. J., and Turner, D. H. (2000) Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA, Biochemistry 39, 9257-9274.
-
(2000)
Biochemistry
, vol.39
, pp. 9257-9274
-
-
Schroeder, S.J.1
Turner, D.H.2
-
11
-
-
0025900996
-
Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
-
Peritz, A. E., Kierzek, R., Sugimoto, N., and Turner, D. H. (1991) Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops, Biochemistry 30, 6428-6436.
-
(1991)
Biochemistry
, vol.30
, pp. 6428-6436
-
-
Peritz, A.E.1
Kierzek, R.2
Sugimoto, N.3
Turner, D.H.4
-
12
-
-
0028071557
-
Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures - 1994
-
Gutell, R. R. (1994) Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures - 1994, Nucleic Acids Res. 22, 3502-3507.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3502-3507
-
-
Gutell, R.R.1
-
13
-
-
0027225783
-
A compilation of large subunit (23s-like and 23s-like) ribosomal-RNA structures - 1993
-
Gutell, R. R., Gray, M. W., and Schnare, M. N. (1993) A compilation of large subunit (23s-like and 23s-like) ribosomal-RNA structures - 1993, Nucleic Acids Res. 21, 3055-3074.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 3055-3074
-
-
Gutell, R.R.1
Gray, M.W.2
Schnare, M.N.3
-
14
-
-
0029877001
-
Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA
-
Schnare, M. N., Damberger, S. H., Gray, M. W., and Gutell, R. R. (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA, J. Mol. Biol. 256, 701-719.
-
(1996)
J. Mol. Biol
, vol.256
, pp. 701-719
-
-
Schnare, M.N.1
Damberger, S.H.2
Gray, M.W.3
Gutell, R.R.4
-
15
-
-
0031866152
-
5S rRNA data bank
-
Szymanski, M., Specht, T., Barciszewska, M. Z., Barciszewski, J., and Erdmann, V. A. (1998) 5S rRNA data bank, Nucleic Acids Res. 26, 156-159.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 156-159
-
-
Szymanski, M.1
Specht, T.2
Barciszewska, M.Z.3
Barciszewski, J.4
Erdmann, V.A.5
-
16
-
-
0031804156
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. (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
Horn, C.2
Brown, M.3
Ioudovitch, A.4
Steinberg, S.5
-
17
-
-
0031866668
-
The signal recognition particle database (SRPDB)
-
Larsen, N., Samuelsson, T., and Zwieb, C. (1998) The signal recognition particle database (SRPDB), Nucleic Acids Res. 26, 177-178.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 177-178
-
-
Larsen, N.1
Samuelsson, T.2
Zwieb, C.3
-
18
-
-
0031841911
-
The ribonuclease P database
-
Brown, J. W. (1998) The ribonuclease P database, Nucleic Acids Res. 26, 351-352.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 351-352
-
-
Brown, J.W.1
-
19
-
-
0028146967
-
A comparative database of group I intron structures
-
Damberger, S. H., and Gutell, R. R. (1994) A comparative database of group I intron structures, Nucleic Acids Res. 22, 3508-3510.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 3508-3510
-
-
Damberger, S.H.1
Gutell, R.R.2
-
20
-
-
0021256581
-
Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review
-
Waring, R. B., and Davies, R. W. (1984) Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review, Gene 28, 277-291.
-
(1984)
Gene
, vol.28
, pp. 277-291
-
-
Waring, R.B.1
Davies, R.W.2
-
21
-
-
0024428420
-
Comparative and functional-anatomy of group-Ii catalytic introns - A review
-
Michel, F., Umesono, K., and Ozeki, H. (1989) Comparative and functional-anatomy of group-Ii catalytic introns - A review, Gene 82, 5-30.
-
(1989)
Gene
, vol.82
, pp. 5-30
-
-
Michel, F.1
Umesono, K.2
Ozeki, H.3
-
22
-
-
34247526026
-
Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes
-
Wright, D. J., Rice, J. L., Yanker, D. M., and Znosko, B. M. (2007) Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes, Biochemistry 46, 4625-4634.
-
(2007)
Biochemistry
, vol.46
, pp. 4625-4634
-
-
Wright, D.J.1
Rice, J.L.2
Yanker, D.M.3
Znosko, B.M.4
-
24
-
-
34247503267
-
-
3.5: Melt Curve Processing Program
-
McDowell, J. A. (1996) MeltWin v. 3.5: Melt Curve Processing Program.
-
(1996)
MeltWin v
-
-
McDowell, J.A.1
-
25
-
-
0020674698
-
Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
-
Petersheim, M., and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp, Biochemistry 22, 256-263.
-
(1983)
Biochemistry
, vol.22
, pp. 256-263
-
-
Petersheim, M.1
Turner, D.H.2
-
26
-
-
0029805937
-
2 by two-dimensional NMR and simulated annealing
-
2 by two-dimensional NMR and simulated annealing, Biochemistry 35, 14077-14089.
-
(1996)
Biochemistry
, vol.35
, pp. 14077-14089
-
-
McDowell, J.A.1
Turner, D.H.2
-
27
-
-
0016189342
-
Stability of ribonucleic-acid double-stranded helices
-
Borer, P. N., Dengler, B., Tinoco, I., and Uhlenbeck, O. (1974) Stability of ribonucleic-acid double-stranded helices, J. Mol. Biol. 86, 843-853.
-
(1974)
J. Mol. Biol
, vol.86
, pp. 843-853
-
-
Borer, P.N.1
Dengler, B.2
Tinoco, I.3
Uhlenbeck, O.4
-
28
-
-
0029382234
-
GU base-pairing motifs in ribosomal-RNA
-
Gautheret, D., Konings, D., and Gutell, R. R. (1995) GU base-pairing motifs in ribosomal-RNA, RNA 1, 807-814.
-
(1995)
RNA
, vol.1
, pp. 807-814
-
-
Gautheret, D.1
Konings, D.2
Gutell, R.R.3
-
29
-
-
0028085964
-
The stability and structure of tandem GA mismatches in RNA depend on closing base pairs
-
Walter, A. E., Wu, M., and Turner, D. H. (1994) The stability and structure of tandem GA mismatches in RNA depend on closing base pairs, Biochemistry 33, 11349-11354.
-
(1994)
Biochemistry
, vol.33
, pp. 11349-11354
-
-
Walter, A.E.1
Wu, M.2
Turner, D.H.3
-
30
-
-
0025925206
-
-
SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs, Biochemistry 30, 8242-8251.
-
SantaLucia, J., Jr., Kierzek, R., and Turner, D. H. (1991) Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs, Biochemistry 30, 8242-8251.
-
-
-
-
31
-
-
12044257509
-
Functional-group substitutions as probes of hydrogen-bonding between GA mismatches in RNA internal loops
-
SantaLucia, J., Kierzek, R., and Turner, D. H. (1991) Functional-group substitutions as probes of hydrogen-bonding between GA mismatches in RNA internal loops, J. Am. Chem. Soc. 113, 4313-4322.
-
(1991)
J. Am. Chem. Soc
, vol.113
, pp. 4313-4322
-
-
SantaLucia, J.1
Kierzek, R.2
Turner, D.H.3
-
32
-
-
0027146665
-
2 in solution from NMR and restrained molecular dynamics
-
2 in solution from NMR and restrained molecular dynamics, Biochemistry 32, 12612-23.
-
(1993)
Biochemistry
, vol.32
, pp. 12612-12623
-
-
SantaLucia Jr., J.1
Turner, D.H.2
-
33
-
-
0028917227
-
A periodic table of symmetric tandem mismatches in RNA
-
Wu, M., McDowell, J. A., and Turner, D. H. (1995) A periodic table of symmetric tandem mismatches in RNA, Biochemistry 34, 3204-3211.
-
(1995)
Biochemistry
, vol.34
, pp. 3204-3211
-
-
Wu, M.1
McDowell, J.A.2
Turner, D.H.3
-
34
-
-
0025186882
-
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
-
Longfellow, C. E., Kierzek, R., and Turner, D. H. (1990) Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides, Biochemistry 29, 278-285.
-
(1990)
Biochemistry
, vol.29
, pp. 278-285
-
-
Longfellow, C.E.1
Kierzek, R.2
Turner, D.H.3
-
35
-
-
0033607261
-
Thermodynamics of single mismatches in RNA duplexes
-
Kierzek, R., Burkard, M. E., and Turner, D. H. (1999) Thermodynamics of single mismatches in RNA duplexes, Biochemistry 38, 14214-14223.
-
(1999)
Biochemistry
, vol.38
, pp. 14214-14223
-
-
Kierzek, R.1
Burkard, M.E.2
Turner, D.H.3
-
36
-
-
33746320475
-
Revolutions in RNA secondary structure prediction
-
Mathews, D. H. (2006) Revolutions in RNA secondary structure prediction, J. Mol. Biol. 359, 526-532.
-
(2006)
J. Mol. Biol
, vol.359
, pp. 526-532
-
-
Mathews, D.H.1
|