-
2
-
-
69049103112
-
The RNA structure alignment ontology
-
Brown JW, Birmingham A, Griffiths PE, Jossinet F, Kachouri-Lafond R, Knight R, Lang BF, Leontis N, Steger G, Stombaugh J, et al. 2009. The RNA structure alignment ontology. RNA 15: 1623-1631.
-
(2009)
RNA
, vol.15
, pp. 1623-1631
-
-
Brown, J.W.1
Birmingham, A.2
Griffiths, P.E.3
Jossinet, F.4
Kachouri-Lafond, R.5
Knight, R.6
Lang, B.F.7
Leontis, N.8
Steger, G.9
Stombaugh, J.10
-
3
-
-
0027995790
-
Isolation of RNA aptamers for biological cofactors by in vitro selection
-
Burgstaller P, Famulok M. 1994. Isolation of RNA aptamers for biological cofactors by in vitro selection. Angew Chem Int Ed Engl 33: 1084-1087.
-
(1994)
Angew Chem Int Ed Engl
, vol.33
, pp. 1084-1087
-
-
Burgstaller, P.1
Famulok, M.2
-
4
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
doi: 10.1186/ 1471-2105-3-2
-
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM, 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 Bioinformatics 3: 2. doi: 10.1186/ 1471-2105-3-2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Muller, K.M.10
-
5
-
-
0036865381
-
The Neurospora Varkud satellite ribozyme
-
Collins RA. 2002. The Neurospora Varkud satellite ribozyme. Biochem Soc Trans 30: 1122-1126.
-
(2002)
Biochem Soc Trans
, vol.30
, pp. 1122-1126
-
-
Collins, R.A.1
-
6
-
-
79957851139
-
Sequence-based identification of 3D structural modules in RNA with RMDetect
-
Cruz JA, Westhof E. 2011. Sequence-based identification of 3D structural modules in RNA with RMDetect. Nat Methods 8: 513-521.
-
(2011)
Nat Methods
, vol.8
, pp. 513-521
-
-
Cruz, J.A.1
Westhof, E.2
-
7
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar RC. 2004. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
8
-
-
0029943824
-
In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding region
-
Famulok M, Huttenhofer A. 1996. In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding region. Biochemistry 35: 4265-4270.
-
(1996)
Biochemistry
, vol.35
, pp. 4265-4270
-
-
Famulok, M.1
Huttenhofer, A.2
-
9
-
-
0038606979
-
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design
-
Gan HH, Pasquali S, Schlick T. 2003. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res 31: 2926-2943.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2926-2943
-
-
Gan, H.H.1
Pasquali, S.2
Schlick, T.3
-
10
-
-
17844386108
-
A benchmark of multiple sequence alignment programs upon structural RNAs
-
Gardner PP, Wilm A, Washietl S. 2005. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res 33: 2433-2439.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 2433-2439
-
-
Gardner, P.P.1
Wilm, A.2
Washietl, S.3
-
11
-
-
21844467243
-
In vitro RNA random pools are not structurally diverse: A computational analysis
-
Gevertz J, Gan HH, Schlick T. 2005. In vitro RNA random pools are not structurally diverse: A computational analysis. RNA 11: 853-863.
-
(2005)
RNA
, vol.11
, pp. 853-863
-
-
Gevertz, J.1
Gan, H.H.2
Schlick, T.3
-
12
-
-
0034724565
-
Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting
-
Giedroc DP, Theimer CA, Nixon PL. 2000. Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting. J Mol Biol 298: 167-185.
-
(2000)
J Mol Biol
, vol.298
, pp. 167-185
-
-
Giedroc, D.P.1
Theimer, C.A.2
Nixon, P.L.3
-
13
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. 2003. Rfam: An RNA family database. Nucleic Acids Res 31: 439-441.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
14
-
-
0027304542
-
Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA
-
Guo HC, De Abreu DM, Tillier ER, Saville BJ, Olive JE, Collins RA. 1993. Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA. J Mol Biol 232: 351-361.
-
(1993)
J Mol Biol
, vol.232
, pp. 351-361
-
-
Guo, H.C.1
De Abreu, D.M.2
Tillier, E.R.3
Saville, B.J.4
Olive, J.E.5
Collins, R.A.6
-
15
-
-
79959310410
-
The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
-
Hoehndorf R, Batchelor C, Bittner T, Dumontier M, Eilbeck K, Knight R, Mungall CJ, Richardson JS, Stombaugh J, Westhof E, et al. 2011. The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Appl Ontol 6: 53-89.
-
(2011)
Appl Ontol
, vol.6
, pp. 53-89
-
-
Hoehndorf, R.1
Batchelor, C.2
Bittner, T.3
Dumontier, M.4
Eilbeck, K.5
Knight, R.6
Mungall, C.J.7
Richardson, J.S.8
Stombaugh, J.9
Westhof, E.10
-
16
-
-
33746655784
-
The architectonics of programmable RNA and DNA nanostructures
-
Jaeger L, Chworos A. 2006. The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol 16: 531-543.
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 531-543
-
-
Jaeger, L.1
Chworos, A.2
-
17
-
-
0028224199
-
High-resolution molecular discrimination by RNA
-
Jenison RD, Gill SC, Pardi A, Polisky B. 1994. High-resolution molecular discrimination by RNA. Science 263: 1425-1429.
-
(1994)
Science
, vol.263
, pp. 1425-1429
-
-
Jenison, R.D.1
Gill, S.C.2
Pardi, A.3
Polisky, B.4
-
18
-
-
0029946537
-
Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex
-
Jiang F, Kumar RA, Jones RA, Patel DJ. 1996. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature 382: 183-186.
-
(1996)
Nature
, vol.382
, pp. 183-186
-
-
Jiang, F.1
Kumar, R.A.2
Jones, R.A.3
Patel, D.J.4
-
19
-
-
0030887815
-
Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex
-
Jiang L, Suri AK, Fiala R, Patel DJ. 1997. Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex. Chem Biol 4: 35-50.
-
(1997)
Chem Biol
, vol.4
, pp. 35-50
-
-
Jiang, L.1
Suri, A.K.2
Fiala, R.3
Patel, D.J.4
-
20
-
-
0033565449
-
Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer
-
Jiang L, Majumdar A, Hu W, Jaishree TJ, Xu W, Patel DJ. 1999. Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer. Structure 7: 817-827.
-
(1999)
Structure
, vol.7
, pp. 817-827
-
-
Jiang, L.1
Majumdar, A.2
Hu, W.3
Jaishree, T.J.4
Xu, W.5
Patel, D.J.6
-
21
-
-
77955405123
-
Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
-
Jossinet F, Ludwig TE, Westhof E. 2010. Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26: 2057-2059.
-
(2010)
Bioinformatics
, vol.26
, pp. 2057-2059
-
-
Jossinet, F.1
Ludwig, T.E.2
Westhof, E.3
-
22
-
-
58149191272
-
tRNAdb 2009: Compilation of tRNA sequences and tRNA genes
-
Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J. 2009. tRNAdb 2009: Compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 37: D159-D162.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Juhling, F.1
Morl, M.2
Hartmann, R.K.3
Sprinzl, M.4
Stadler, P.F.5
Putz, J.6
-
23
-
-
0033452721
-
Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency
-
Kim YG, Su L, Maas S, O'Neill A, Rich A. 1999. Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency. Proc Natl Acad Sci 96: 14234-14239.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 14234-14239
-
-
Kim, Y.G.1
Su, L.2
Maas, S.3
O'Neill, A.4
Rich, A.5
-
24
-
-
0033860774
-
Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses
-
Kim YG, Maas S, Wang SC, Rich A. 2000. Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses. RNA 6: 1157-1165.
-
(2000)
RNA
, vol.6
, pp. 1157-1165
-
-
Kim, Y.G.1
Maas, S.2
Wang, S.C.3
Rich, A.4
-
25
-
-
27144468672
-
Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids
-
Knight R, De Sterck H, Markel R, Smit S, Oshmyansky A, Yarus M. 2005. Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids. Nucleic Acids Res 33: 5924-5935.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5924-5935
-
-
Knight, R.1
De Sterck, H.2
Markel, R.3
Smit, S.4
Oshmyansky, A.5
Yarus, M.6
-
28
-
-
0032300804
-
Conserved geometrical base-pairing patterns in RNA
-
Leontis NB, Westhof E. 1998. Conserved geometrical base-pairing patterns in RNA. Q Rev Biophys 31: 399-455.
-
(1998)
Q Rev Biophys
, vol.31
, pp. 399-455
-
-
Leontis, N.B.1
Westhof, E.2
-
29
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
Leontis NB, Westhof E. 2001. Geometric nomenclature and classification of RNA base pairs. RNA 7: 499-512.
-
(2001)
RNA
, vol.7
, pp. 499-512
-
-
Leontis, N.B.1
Westhof, E.2
-
31
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis NB, Stombaugh J, Westhof E. 2002. The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res 30: 3497-3531.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3497-3531
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
32
-
-
33748955920
-
Structural constraints and mutational bias in the evolutionary restoration of a severe deletion in RNA phage MS2
-
Licis N, van Duin J. 2006. Structural constraints and mutational bias in the evolutionary restoration of a severe deletion in RNA phage MS2. J Mol Evol 63: 314-329.
-
(2006)
J Mol Evol
, vol.63
, pp. 314-329
-
-
Licis, N.1
Van Duin, J.2
-
33
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
Loytynoja A, Goldman N. 2008. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.
-
(2008)
Science
, vol.320
, pp. 1632-1635
-
-
Loytynoja, A.1
Goldman, N.2
-
36
-
-
36448954303
-
FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
-
Sarver M, Zirbel CL, Stombaugh J, Mokdad A, Leontis NB. 2008. FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures. J Math Biol 56: 215-252.
-
(2008)
J Math Biol
, vol.56
, pp. 215-252
-
-
Sarver, M.1
Zirbel, C.L.2
Stombaugh, J.3
Mokdad, A.4
Leontis, N.B.5
-
37
-
-
0033102314
-
A small catalytic RNA motif with Diels- Alderase activity
-
Seelig B, Jaschke A. 1999. A small catalytic RNA motif with Diels- Alderase activity. Chem Biol 6: 167-176.
-
(1999)
Chem Biol
, vol.6
, pp. 167-176
-
-
Seelig, B.1
Jaschke, A.2
-
38
-
-
29844452150
-
Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories
-
Smit S, Yarus M, Knight R. 2006. Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories. RNA 12: 1-14.
-
(2006)
RNA
, vol.12
, pp. 1-14
-
-
Smit, S.1
Yarus, M.2
Knight, R.3
-
39
-
-
34250880169
-
Evolutionary rates vary among rRNA structural elements
-
Smit S, Widmann J, Knight R. 2007. Evolutionary rates vary among rRNA structural elements. Nucleic Acids Res 35: 3339-3354.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3339-3354
-
-
Smit, S.1
Widmann, J.2
Knight, R.3
-
40
-
-
63249135361
-
RNA structure prediction from evolutionary patterns of nucleotide composition
-
Smit S, Knight R, Heringa J. 2009. RNA structure prediction from evolutionary patterns of nucleotide composition. Nucleic Acids Res 37: 1378-1386.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 1378-1386
-
-
Smit, S.1
Knight, R.2
Heringa, J.3
-
42
-
-
79958166117
-
Boulder ALignment Editor (ALE): A web-based RNA alignment tool
-
Stombaugh J, Widmann J, McDonald D, Knight R. 2011. Boulder ALignment Editor (ALE): A web-based RNA alignment tool. Bioinformatics 27: 1706-1707.
-
(2011)
Bioinformatics
, vol.27
, pp. 1706-1707
-
-
Stombaugh, J.1
Widmann, J.2
McDonald, D.3
Knight, R.4
-
43
-
-
23444442072
-
MAO: A Multiple Alignment Ontology for nucleic acid and protein sequences
-
Thompson JD, Holbrook SR, Katoh K, Koehl P, Moras D, Westhof E, Poch O. 2005. MAO: A Multiple Alignment Ontology for nucleic acid and protein sequences. Nucleic Acids Res 33: 4164-4171.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 4164-4171
-
-
Thompson, J.D.1
Holbrook, S.R.2
Katoh, K.3
Koehl, P.4
Moras, D.5
Westhof, E.6
Poch, O.7
-
45
-
-
0036606141
-
Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes
-
Wang HC, Hickey DA. 2002. Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes. Nucleic Acids Res 30: 2501-2507.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 2501-2507
-
-
Wang, H.C.1
Hickey, D.A.2
-
46
-
-
0029294539
-
Specific binding of aminoglycoside antibiotics to RNA
-
Wang Y, Rando RR. 1995. Specific binding of aminoglycoside antibiotics to RNA. Chem Biol 2: 281-290.
-
(1995)
Chem Biol
, vol.2
, pp. 281-290
-
-
Wang, Y.1
Rando, R.R.2
-
47
-
-
0029766901
-
RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities
-
Wang Y, Killian J, Hamasaki K, Rando RR. 1996. RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities. Biochemistry 35: 12338-12346.
-
(1996)
Biochemistry
, vol.35
, pp. 12338-12346
-
-
Wang, Y.1
Killian, J.2
Hamasaki, K.3
Rando, R.R.4
-
48
-
-
0032514717
-
Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot
-
Wilson C, Nix J, Szostak J. 1998. Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot. Biochemistry 37: 14410-14419.
-
(1998)
Biochemistry
, vol.37
, pp. 14410-14419
-
-
Wilson, C.1
Nix, J.2
Szostak, J.3
-
50
-
-
0029972909
-
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy
-
Yang Y, Kochoyan M, Burgstaller P, Westhof E, Famulok M. 1996. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science 272: 1343-1347.
-
(1996)
Science
, vol.272
, pp. 1343-1347
-
-
Yang, Y.1
Kochoyan, M.2
Burgstaller, P.3
Westhof, E.4
Famulok, M.5
-
51
-
-
0033781246
-
Peptidyl transferase: Ancient and exiguous
-
Yarus M, Welch M. 2000. Peptidyl transferase: Ancient and exiguous. Chem Biol 7: R187-R190.
-
(2000)
Chem Biol
, vol.7
-
-
Yarus, M.1
Welch, M.2
-
52
-
-
0030752211
-
Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
-
Zimmermann GR, Jenison RD, Wick CL, Simorre JP, Pardi A. 1997. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nat Struct Biol 4: 644-649.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 644-649
-
-
Zimmermann, G.R.1
Jenison, R.D.2
Wick, C.L.3
Simorre, J.P.4
Pardi, A.5
|