-
1
-
-
84916625049
-
An introduction to recurrent nucleotide interactions in RNA
-
Sweeney,B.A., Roy,P. and Leontis,N.B. (2015) An introduction to recurrent nucleotide interactions in RNA. Wiley Interdiscip. Rev. RNA, 6, 17-45.
-
(2015)
Wiley Interdiscip. Rev. RNA
, vol.6
, pp. 17-45
-
-
Sweeney, B.A.1
Roy, P.2
Leontis, N.B.3
-
2
-
-
0036760665
-
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules
-
Leontis,N.B., Stombaugh,J. and Westhof,E. (2002) Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie, 84, 961-973.
-
(2002)
Biochimie
, vol.84
, pp. 961-973
-
-
Leontis, N.B.1
Stombaugh, J.2
Westhof, E.3
-
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
-
-
84934438960
-
UNAFold: Software for nucleic acid folding and hybridization
-
Markham,N.R. and Zuker,M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
-
(2008)
Methods Mol. Biol.
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
5
-
-
82055164092
-
ViennaRNA package 2.0
-
Lorenz,R., Bernhart,S.H., Honer Zu Siederdissen,C., Tafer,H., Flamm,C., Stadler,P.F. and Hofacker,I.L. (2011) ViennaRNA Package 2.0. AMB, 6, 26.
-
(2011)
AMB
, vol.6
, pp. 26
-
-
Lorenz, R.1
Bernhart, S.H.2
Honer Zu Siederdissen, C.3
Tafer, H.4
Flamm, C.5
Stadler, P.F.6
Hofacker, I.L.7
-
6
-
-
84859947721
-
LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs
-
Will,S., Joshi,T., Hofacker,I.L., Stadler,P.F. and Backofen,R. (2012) LocARNA-P: accurate boundary prediction and improved detection of structural RNAs. RNA, 18, 900-914.
-
(2012)
RNA
, vol.18
, pp. 900-914
-
-
Will, S.1
Joshi, T.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
7
-
-
84863522073
-
Towards 3D structure prediction of large RNA molecules: An integer programming framework to insert local 3D motifs in RNA secondary structure
-
Reinharz,V.,Major,F. and Waldispuhl,J. (2012) Towards 3D structure prediction of large RNA molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure. Bioinformatics, 28, i207-i214.
-
(2012)
Bioinformatics
, vol.28
, pp. i207-i214
-
-
Reinharz, V.1
Major, F.2
Waldispuhl, J.3
-
8
-
-
17844366343
-
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments
-
Lescoute,A., Leontis,N.B., Massire,C. and Westhof,E. (2005) Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments. Nucleic Acids Res., 33, 2395-2409.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2395-2409
-
-
Lescoute, A.1
Leontis, N.B.2
Massire, C.3
Westhof, E.4
-
9
-
-
84876554720
-
Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking
-
Leontis,NB and Westhof,E (eds) Springer Berlin; NY
-
Zirbel,C.L. and Leontis,N.B. (2012) Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and Benchmarking. In: Leontis,NB and Westhof,E (eds). RNA 3D structure analysis and prediction. Springer, Berlin; NY, Vol. 27, pp. 281-298.
-
(2012)
RNA. 3D Structure Analysis and Prediction
, vol.27
, pp. 281-298
-
-
Zirbel, C.L.1
Leontis, N.B.2
-
10
-
-
84884679567
-
Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas
-
Petrov,A.I., Zirbel,C.L. and Leontis,N.B. (2013) Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas. RNA, 19, 1327-1340.
-
(2013)
RNA
, vol.19
, pp. 1327-1340
-
-
Petrov, A.I.1
Zirbel, C.L.2
Leontis, N.B.3
-
11
-
-
65549163541
-
Frequency and isostericity of RNA base pairs
-
Stombaugh,J., Zirbel,C.L., Westhof,E. and Leontis,N.B. (2009) Frequency and isostericity of RNA base pairs. Nucleic Acids Res., 37, 2294-2312.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2294-2312
-
-
Stombaugh, J.1
Zirbel, C.L.2
Westhof, E.3
Leontis, N.B.4
-
12
-
-
69849114530
-
Classification and energetics of the base-phosphate interactions in RNA
-
Zirbel,C.L., Sponer,J.E., Sponer,J., Stombaugh,J. and Leontis,N.B. (2009) Classification and energetics of the base-phosphate interactions in RNA. Nucleic Acids Res., 37, 4898-4918.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 4898-4918
-
-
Zirbel, C.L.1
Sponer, J.E.2
Sponer, J.3
Stombaugh, J.4
Leontis, N.B.5
-
13
-
-
0035010211
-
Geometric nomenclature and classification of RNA base pairs
-
Leontis,N.B. and 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
-
14
-
-
84890336914
-
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments
-
Theis,C., Honer Zu Siederdissen,C., Hofacker,I.L. and Gorodkin,J. (2013) Automated identification of RNA 3D modules with discriminative power in RNA structural alignments. Nucleic Acids Res., 41, 9999-10009.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 9999-10009
-
-
Theis, C.1
Honer Zu Siederdissen, C.2
Hofacker, I.L.3
Gorodkin, J.4
-
15
-
-
79957851139
-
Sequence-based identification of 3D structural modules in RNA with RMDetect
-
Cruz,J.A. and 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
-
17
-
-
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
-
18
-
-
0028593508
-
Stochastic context-free grammars for tRNA modeling
-
Sakakibara,Y., Brown,M., Hughey,R., Mian,I.S., Sjolander,K., Underwood,R.C. and Haussler,D. (1994) Stochastic context-free grammars for tRNA modeling. Nucleic Acids Res., 22, 5112-5120.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5112-5120
-
-
Sakakibara, Y.1
Brown, M.2
Hughey, R.3
Mian, I.S.4
Sjolander, K.5
Underwood, R.C.6
Haussler, D.7
-
19
-
-
65549111754
-
Infernal 1.0: Inference of RNA alignments
-
Nawrocki,E.P., Kolbe,D.L. and Eddy,S.R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
Kolbe, D.L.2
Eddy, S.R.3
-
20
-
-
84890037468
-
Infernal 1.1: 100-fold faster RNA homology searches
-
Nawrocki,E.P. and Eddy,S.R. (2013) Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29, 2933-2935.
-
(2013)
Bioinformatics
, vol.29
, pp. 2933-2935
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
21
-
-
84874266637
-
Rfam 11.0: 10 years of RNA families
-
Burge,S.W., Daub,J., Eberhardt,R., Tate,J., Barquist,L., Nawrocki,E.P., Eddy,S.R., Gardner,P.P. and Bateman,A. (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D226-D232
-
-
Burge, S.W.1
Daub, J.2
Eberhardt, R.3
Tate, J.4
Barquist, L.5
Nawrocki, E.P.6
Eddy, S.R.7
Gardner, P.P.8
Bateman, A.9
-
22
-
-
84946094179
-
Rfam 12.0: Updates to the RNA families database
-
Nawrocki,E.P., Burge,S.W., Bateman,A., Daub,J., Eberhardt,R.Y., Eddy,S.R., Floden,E.W., Gardner,P.P., Jones,T.A., Tate,J. et al. (2014) Rfam 12.0: updates to the RNA families database. Nucleic Acids Res., 43, D130-D137.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. D130-D137
-
-
Nawrocki, E.P.1
Burge, S.W.2
Bateman, A.3
Daub, J.4
Eberhardt, R.Y.5
Eddy, S.R.6
Floden, E.W.7
Gardner, P.P.8
Jones, T.A.9
Tate, J.10
-
23
-
-
84941062157
-
Annotating RNA motifs in sequences and alignments
-
Gardner,P.P. and Eldai,H. (2014) Annotating RNA motifs in sequences and alignments. Nucleic Acids Res., 43, 691-698.
-
(2014)
Nucleic Acids Res.
, vol.43
, pp. 691-698
-
-
Gardner, P.P.1
Eldai, H.2
-
25
-
-
84884603324
-
Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
-
Kamisetty,H., Ovchinnikov,S. and Baker,D. (2013) Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc. Natl. Acad. Sci. U.S.A., 110, 15674-15679.
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 15674-15679
-
-
Kamisetty, H.1
Ovchinnikov, S.2
Baker, D.3
-
26
-
-
84857838609
-
Comprehensive survey and geometric classification of base triples in RNA structures
-
Abu Almakarem,A.S., Petrov,A.I., Stombaugh,J., Zirbel,C.L. and Leontis,N.B. (2012) Comprehensive survey and geometric classification of base triples in RNA structures. Nucleic Acids Res., 40, 1407-1423.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1407-1423
-
-
Abu Almakarem, A.S.1
Petrov, A.I.2
Stombaugh, J.3
Zirbel, C.L.4
Leontis, N.B.5
-
27
-
-
84873739311
-
The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
-
Quast,C., Pruesse,E., Yilmaz,P., Gerken,J., Schweer,T., Yarza,P., Peplies,J. and Glockner,F.O. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res., 41, D590-D596.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D590-D596
-
-
Quast, C.1
Pruesse, E.2
Yilmaz, P.3
Gerken, J.4
Schweer, T.5
Yarza, P.6
Peplies, J.7
Glockner, F.O.8
-
28
-
-
33746061683
-
Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB
-
DeSantis,T.Z., Hugenholtz,P., Larsen,N., Rojas,M., Brodie,E.L., Keller,K., Huber,T., Dalevi,D., Hu,P. and Andersen,G.L. (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
-
(2006)
Appl. Environ. Microbiol.
, vol.72
, pp. 5069-5072
-
-
DeSantis, T.Z.1
Hugenholtz, P.2
Larsen, N.3
Rojas, M.4
Brodie, E.L.5
Keller, K.6
Huber, T.7
Dalevi, D.8
Hu, P.9
Andersen, G.L.10
-
29
-
-
36448954303
-
FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
-
Sarver,M., Zirbel,C.L., Stombaugh,J., Mokdad,A. and Leontis,N.B. (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
-
30
-
-
13244260785
-
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
-
Dowell,R.D. and Eddy,S.R. (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics, 5, 71.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 71
-
-
Dowell, R.D.1
Eddy, S.R.2
-
31
-
-
70350004178
-
The era of RNA awakening: Structural biology of RNA in the early years
-
Rich,A. (2009) The era of RNA awakening: structural biology of RNA in the early years. Q. Rev. Biophys., 42, 117-137.
-
(2009)
Q. Rev. Biophys.
, vol.42
, pp. 117-137
-
-
Rich, A.1
-
32
-
-
0036717041
-
Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs
-
Nagaswamy,U. and Fox,G.E. (2002) Frequent occurrence of the T-loop RNA folding motif in ribosomal RNAs. RNA, 8, 1112-1119.
-
(2002)
RNA
, vol.8
, pp. 1112-1119
-
-
Nagaswamy, U.1
Fox, G.E.2
-
33
-
-
78650096290
-
Quantum chemical studies of nucleic acids: Can we construct a bridge to the RNA structural biology and bioinformatics communities? J
-
Sponer,J., Sponer,J.E., Petrov,A.I. and Leontis,N.B. (2010) Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities? J. Phys. Chem. B, 114, 15723-15741.
-
(2010)
Phys. Chem. B
, vol.114
, pp. 15723-15741
-
-
Sponer, J.1
Sponer, J.E.2
Petrov, A.I.3
Leontis, N.B.4
|