-
1
-
-
0030763907
-
RNA aptamers
-
Heus, H.A. (1997) RNA aptamers. Nat. Struct. Biol., 4, 597-600.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 597-600
-
-
Heus, H.A.1
-
2
-
-
0025194307
-
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
-
Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249, 505-510.
-
(1990)
Science
, vol.249
, pp. 505-510
-
-
Tuerk, C.1
Gold, L.2
-
3
-
-
33744469562
-
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
-
Thore, S., Leibundgut, M. and Ban, N. (2006) Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science, 312, 1208-1211.
-
(2006)
Science
, vol.312
, pp. 1208-1211
-
-
Thore, S.1
Leibundgut, M.2
Ban, N.3
-
4
-
-
33746228126
-
Tertiary contacts distant from the active site prime a ribozyme for catalysis
-
Martick, M. and Scott, W. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell, 126, 309-320.
-
(2006)
Cell
, vol.126
, pp. 309-320
-
-
Martick, M.1
Scott, W.2
-
5
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A., Do, R. and Sali, A. (2000) Modeling of loops in protein structures. Prot. Sci., 9, 1753-1773.
-
(2000)
Prot. Sci.
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.2
Sali, A.3
-
6
-
-
58149191274
-
Rfam: updates to the RNA families database
-
Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
-
7
-
-
0026742978
-
The nucleic acid database. a comprehensive relational database of three-dimensional structures of nucleic acids
-
Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S., Srinivasan, A. and Schneider, B. (1992) The nucleic acid database. a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
-
(1992)
Biophys. J.
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.7
Srinivasan, A.8
Schneider, B.9
-
8
-
-
15444372483
-
The application of cluster analysis in the intercomparison of loop structures in RNA
-
Huang, H.-C., Nagaswamy, U. and Fox, G.E. (2005) The application of cluster analysis in the intercomparison of loop structures in RNA. RNA, 11, 412-423.
-
(2005)
RNA
, vol.11
, pp. 412-423
-
-
Huang, H.-C.1
Nagaswamy, U.2
Fox, G.E.3
-
9
-
-
34548342932
-
A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence-structure relationships
-
Lisi, V. and Major, F. (2007) A comparative analysis of the triloops in all high-resolution RNA structures reveals sequence-structure relationships. RNA, 13, 1537-1545.
-
(2007)
RNA
, vol.13
, pp. 1537-1545
-
-
Lisi, V.1
Major, F.2
-
10
-
-
22044438679
-
Describing RNA structure by libraries of clustered nucleotide doublets
-
Sykes, M.T. and Levitt, M. (2005) Describing RNA structure by libraries of clustered nucleotide doublets. J. Mol. Biol., 351, 26-38.
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 26-38
-
-
Sykes, M.T.1
Levitt, M.2
-
11
-
-
40449091092
-
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution)
-
Richardson, J.S., Schneider, B., Murray, L.W., Kapral, G.J., Immormino, R.M., Headd, J.J., Richardson, D.C., Ham, D., Hershkovits, E., Williams, L.D. et al. (2008) RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). RNA, 14, 465-481.
-
(2008)
RNA
, vol.14
, pp. 465-481
-
-
Richardson, J.S.1
Schneider, B.2
Murray, L.W.3
Kapral, G.J.4
Immormino, R.M.5
Headd, J.J.6
Richardson, D.C.7
Ham, D.8
Hershkovits, E.9
Williams, L.D.10
-
12
-
-
0037102491
-
The non-Watson-Crick base pairs and their associated isostericity matrices
-
Leontis, N.B., Stombaugh, J. and 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
-
13
-
-
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., 7, 2294-2312.
-
(2009)
Nucleic Acids Res.
, vol.7
, pp. 2294-2312
-
-
Stombaugh, J.1
Zirbel, C.L.2
Westhof, E.3
Leontis, N.B.4
-
14
-
-
0032232529
-
MANIP: an interactive tool for modelling RNA
-
Massire, C. and Westhof, E. (1998) MANIP: an interactive tool for modelling RNA. J. Mol. Graph Model, 16, 197-205, 255-257.
-
(1998)
J. Mol. Graph Model
, vol.16
, Issue.197-205
, pp. 255-257
-
-
Massire, C.1
Westhof, E.2
-
15
-
-
25144458057
-
Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure
-
Jossinet, F. and Westhof, E. (2005) Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics, 21, 3320-3321.
-
(2005)
Bioinformatics
, vol.21
, pp. 3320-3321
-
-
Jossinet, F.1
Westhof, E.2
-
16
-
-
0345983583
-
Modeling unusual nucleic acid structures
-
Leontes, N. and SantaLucia, J. Jr (eds), American Chemical Society, Washington, DC
-
Macke, T. and Case, D. (1998) Modeling unusual nucleic acid structures. In Leontes, N. and SantaLucia, J. Jr (eds), Molecular Modeling of Nucleic Acids. American Chemical Society, Washington, DC, pp. 379-393.
-
(1998)
Molecular Modeling of Nucleic Acids
, pp. 379-393
-
-
Macke, T.1
Case, D.2
-
17
-
-
0242396923
-
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu, X.-J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.-J.1
Olson, W.K.2
-
18
-
-
66249104001
-
Identification and classification of ncRNA molecules using graph properties
-
Childs, L., Nikoloski, Z., May, P. and Walther, D. (2009) Identification and classification of ncRNA molecules using graph properties. Nucleic Acids Res., 37, e66.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Childs, L.1
Nikoloski, Z.2
May, P.3
Walther, D.4
-
19
-
-
41549155036
-
Shape based indexing for faster search of RNA family databases
-
Janssen, S., Reeder, J. and Giegerich, R. (2008) Shape based indexing for faster search of RNA family databases. BMC Bioinformatics, 9, 131.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 131
-
-
Janssen, S.1
Reeder, J.2
Giegerich, R.3
-
20
-
-
35548950310
-
Automated de novo prediction of native-like RNA tertiary structures
-
Das, R. and Baker, D. (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl Assoc. Sci., 104, 14664-14669.
-
(2007)
Proc. Natl Assoc. Sci.
, vol.104
, pp. 14664-14669
-
-
Das, R.1
Baker, D.2
-
21
-
-
44149101971
-
Large scale simulations of 3D RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms
-
Ding, F., Sharma, S., Chalasani, P., Demidov, V.V., Broude, N.E. and Dokholyan, N.V. (2008) Large scale simulations of 3D RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
-
(2008)
RNA
, vol.14
, pp. 1164-1173
-
-
Ding, F.1
Sharma, S.2
Chalasani, P.3
Demidov, V.V.4
Broude, N.E.5
Dokholyan, N.V.6
-
22
-
-
50549096615
-
iFoldRNA: three-dimensional RNA structure prediction and folding
-
Sharma, S., Ding, F. and Dokholyan, N. (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
-
(2008)
Bioinformatics
, vol.24
, pp. 1951-1952
-
-
Sharma, S.1
Ding, F.2
Dokholyan, N.3
-
23
-
-
58249111738
-
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
-
Jonikas, M.A., Radmer, R.J. and Laederach, A. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
-
(2009)
RNA
, vol.15
, pp. 189-199
-
-
Jonikas, M.A.1
Radmer, R.J.2
Laederach, A.3
-
24
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
-
(2008)
Nature
, vol.452
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
25
-
-
0345864010
-
SCOR: structural classification of RNA, version 2.0
-
Tamura, M., Hendrix, D.K., Klosterman, P.S., Schimmelman, N.R.B., Brenner, S.E. and Holbrook, S.R. (2004) SCOR: structural classification of RNA, version 2.0. Nucleic Acids Res., 32, D182-D184.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Tamura, M.1
Hendrix, D.K.2
Klosterman, P.S.3
Schimmelman, N.R.B.4
Brenner, S.E.5
Holbrook, S.R.6
-
26
-
-
38549083634
-
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
-
Bindewald, E., Hayes, R., Yingling, Y.G., Kasprzak, W. and Shapiro, B.A. (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res., 36, D392-D397.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Bindewald, E.1
Hayes, R.2
Yingling, Y.G.3
Kasprzak, W.4
Shapiro, B.A.5
-
27
-
-
38549140073
-
RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures
-
Popenda, M., Blazewicz, M., Szachniuk, M. and Adamiak, R.W. (2008) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res., 36, D386-D391.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Popenda, M.1
Blazewicz, M.2
Szachniuk, M.3
Adamiak, R.W.4
-
28
-
-
55549130811
-
Analysis and classification of RNA tertiary structures
-
Abraham, M., Dror, O., Nussinov, R. and Wolfson, H. (2008) Analysis and classification of RNA tertiary structures. RNA, 14, 2274-2289.
-
(2008)
RNA
, vol.14
, pp. 2274-2289
-
-
Abraham, M.1
Dror, O.2
Nussinov, R.3
Wolfson, H.4
-
29
-
-
1442310610
-
Loops in proteins (LIP)-a comprehensive loop database for homology modelling
-
Michalsky, E., Goede, A. and Preissner, R. (2003) Loops in proteins (LIP)-a comprehensive loop database for homology modelling. Prot Eng, 16, 979-985.
-
(2003)
Prot Eng.
, vol.16
, pp. 979-985
-
-
Michalsky, E.1
Goede, A.2
Preissner, R.3
-
30
-
-
0035906639
-
Quantitative analysis of nucleic acid three-dimensional structures
-
Gendron, P., Lemieux, S. and Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 919-936
-
-
Gendron, P.1
Lemieux, S.2
Major, F.3
-
31
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (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
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
32
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M. and Stiegler, P. (1981) Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 10, 133-148.
-
(1981)
Nucleic Acids Res.
, vol.10
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
33
-
-
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
-
34
-
-
84893482610
-
A solution for the best rotation to relate two sets of vectors
-
Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Cryst., A32, 922-923.
-
(1976)
Acta Cryst.
, vol.A32
, pp. 922-923
-
-
Kabsch, W.1
-
35
-
-
0026030641
-
Database of homology-derived protein structures and the structural meaning of sequence alignment
-
Sander, C. and Schneider, R. (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins, 9, 56-68.
-
(1991)
Proteins
, vol.9
, pp. 56-68
-
-
Sander, C.1
Schneider, R.2
-
36
-
-
15244362640
-
Structural similarity of loops in protein families: toward the understanding of protein evolution
-
Panchenko, A.R. and Madej, T. (2005) Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol. Biol., 5.
-
(2005)
BMC Evol. Biol.
, pp. 5
-
-
Panchenko, A.R.1
Madej, T.2
-
37
-
-
0033134684
-
Protein loops on structurally similar scaffolds: database and conformational analysis
-
Li, W., Liu, Z. and Lai, L. (1999) Protein loops on structurally similar scaffolds: database and conformational analysis. Biopolymers, 49, 481-495.
-
(1999)
Biopolymers
, vol.49
, pp. 481-495
-
-
Li, W.1
Liu, Z.2
Lai, L.3
-
38
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen, E., Goddard, T., Huang, C., Couch, G., Greenblatt, D., Meng, E. and Ferrin, T. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem., 25, 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.1
Goddard, T.2
Huang, C.3
Couch, G.4
Greenblatt, D.5
Meng, E.6
Ferrin, T.7
|