-
1
-
-
0036761417
-
RNA loop-loop interactions as dynamic functional motifs
-
DOI 10.1016/S0300-9084(02)01401-3, PII S0300908402014013
-
C. Brunel, and R. Marquet C. Ehresmann RNA loop-loop interactions as dynamic functional motifs Biochimie 84 2002 925 944 (Pubitemid 35422919)
-
(2002)
Biochimie
, vol.84
, Issue.9
, pp. 925-944
-
-
Brunel, C.1
Marquet, R.2
Romby, P.3
Ehresmann, C.4
-
2
-
-
33746655784
-
The architectonics of programmable RNA and DNA nanostructures
-
DOI 10.1016/j.sbi.2006.07.001, PII S0959440X06001187
-
L. Jaeger, and A. Chworos The architectonics of programmable RNA and DNA nanostructures Curr. Opin. Struct. Biol. 16 2006 531 543 (Pubitemid 44149075)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.4
, pp. 531-543
-
-
Jaeger, L.1
Chworos, A.2
-
3
-
-
34548147103
-
Computational design of an RNA hexagonal nanoring and an RNA nanotube
-
DOI 10.1021/nl070984r
-
Y.G. Yingling, and B.A. Shapiro Computational design of an RNA hexagonal nanoring and an RNA nanotube Nano Lett. 7 2007 2328 2334 (Pubitemid 47310128)
-
(2007)
Nano Letters
, vol.7
, Issue.8
, pp. 2328-2334
-
-
Yingling, Y.G.1
Shapiro, B.A.2
-
4
-
-
65249134554
-
Square-shaped RNA particles from different RNA folds
-
I. Severcan, and C. Geary L. Jaeger Square-shaped RNA particles from different RNA folds Nano Lett. 9 2009 1270 1277
-
(2009)
Nano Lett.
, vol.9
, pp. 1270-1277
-
-
Severcan, I.1
Geary, C.2
Jaeger, L.3
-
5
-
-
24944565527
-
Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology
-
DOI 10.1021/nl051264s
-
A. Khaled, and S.C. Guo P. Guo Controllable self-assembly of nanoparticles for specific delivery of multiple therapeutic molecules to cancer cells using RNA nanotechnology Nano Lett. 5 2005 1797 1808 (Pubitemid 41396168)
-
(2005)
Nano Letters
, vol.5
, Issue.9
, pp. 1797-1808
-
-
Khaled, A.1
Guo, S.2
Li, F.3
Guo, P.4
-
6
-
-
0025861307
-
Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein
-
Y. Eguchi, and J. Tomizawa Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein J. Mol. Biol. 220 1991 831 842
-
(1991)
J. Mol. Biol.
, vol.220
, pp. 831-842
-
-
Eguchi, Y.1
Tomizawa, J.2
-
7
-
-
0029058784
-
Determinants of RNA hairpin loop-loop complex stability
-
R.S. Gregorian Jr. , and D.M. Crothers Determinants of RNA hairpin loop-loop complex stability J. Mol. Biol. 248 1995 968 984
-
(1995)
J. Mol. Biol.
, vol.248
, pp. 968-984
-
-
Gregorian Jr., R.S.1
Crothers, D.M.2
-
8
-
-
77956565237
-
Simulations of RNA interactions with monovalent ions
-
A.A. Chen, and M. Marucho H. Daniel Simulations of RNA interactions with monovalent ions Methods Enzymol. 469 2009 411 432
-
(2009)
Methods Enzymol.
, vol.469
, pp. 411-432
-
-
Chen, A.A.1
Marucho, M.2
Daniel, H.3
-
9
-
-
67649359324
-
The influence of monovalent cation size on the stability of RNA tertiary structures
-
D. Lambert, and D. Leipply D.E. Draper The influence of monovalent cation size on the stability of RNA tertiary structures J. Mol. Biol. 390 2009 791 804
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 791-804
-
-
Lambert, D.1
Leipply, D.2
Draper, D.E.3
-
10
-
-
4944259254
-
Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes
-
DOI 10.1093/nar/gkh841
-
A. Weixlbaumer, and A. Werner R. Schroeder Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes Nucleic Acids Res. 32 2004 5126 5133 (Pubitemid 39445500)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.17
, pp. 5126-5133
-
-
Weixlbaumer, A.1
Werner, A.2
Flamm, C.3
Westhof, E.4
Schroeder, R.5
-
11
-
-
0032827805
-
Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding
-
DOI 10.1017/S1355838299990982
-
F. Jossinet, and J.C. Paillart R. Marquet Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding RNA 5 1999 1222 1234 (Pubitemid 29422764)
-
(1999)
RNA
, vol.5
, Issue.9
, pp. 1222-1234
-
-
Jossinet, F.1
Paillart, J.-C.2
Westhof, E.3
Hermann, T.4
Skripkin, E.5
Lodmell, J.S.6
Ehresmann, C.7
Ehresmann, B.8
Marquet, R.9
-
12
-
-
0031591383
-
The structure of an RNA 'kissing' hairpin complex of the HIV TAR hairpin loop and its complement
-
DOI 10.1006/jmbi.1997.1021
-
K.Y. Chang, and I. Tinoco Jr. The structure of an RNA "kissing" hairpin complex of the HIV TAR hairpin loop and its complement J. Mol. Biol. 269 1997 52 66 (Pubitemid 27243621)
-
(1997)
Journal of Molecular Biology
, vol.269
, Issue.1
, pp. 52-66
-
-
Chang, K.-Y.1
Tinoco Jr., I.2
-
13
-
-
0032528951
-
The solution structure of an RNA loop-loop complex: The ColE1 inverted loop sequence
-
A.J. Lee, and D.M. Crothers The solution structure of an RNA loop-loop complex: the ColE1 inverted loop sequence Structure 6 1998 993 1005 (Pubitemid 28397921)
-
(1998)
Structure
, vol.6
, Issue.8
, pp. 993-1005
-
-
Lee, A.J.1
Crothers, D.M.2
-
14
-
-
42949091948
-
Slight sequence modification unexpectedly alter the metal dependency of a kissing-loop interaction
-
S.P. Ohuchi, and Y. Nakamura Slight sequence modification unexpectedly alter the metal dependency of a kissing-loop interaction Nucleic Acids Symp. Ser. (Oxf). 51 2007 395 396
-
(2007)
Nucleic Acids Symp. Ser. (Oxf).
, vol.51
, pp. 395-396
-
-
Ohuchi, S.P.1
Nakamura, Y.2
-
15
-
-
31544436952
-
Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo
-
DOI 10.1093/nar/gkj435
-
C. Lorenz, N. Piganeau, and R. Schroeder Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo Nucleic Acids Res. 34 2006 334 342 (Pubitemid 43160056)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.1
, pp. 334-342
-
-
Lorenz, C.1
Piganeau, N.2
Schroeder, R.3
-
16
-
-
59649095963
-
A short guide for molecular dynamics simulations of RNA systems
-
Y. Hashem, and P. Auffinger A short guide for molecular dynamics simulations of RNA systems Methods 47 2009 187 197
-
(2009)
Methods
, vol.47
, pp. 187-197
-
-
Hashem, Y.1
Auffinger, P.2
-
17
-
-
16244365573
-
Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita
-
DOI 10.1016/j.jmb.2005.02.015
-
Y.G. Yingling, and B.A. Shapiro Dynamic behavior of the telomerase RNA hairpin structure and its relationship to dyskeratosis congenita J. Mol. Biol. 348 2005 27 42 (Pubitemid 40461838)
-
(2005)
Journal of Molecular Biology
, vol.348
, Issue.1
, pp. 27-42
-
-
Yingling, Y.G.1
Shapiro, B.A.2
-
18
-
-
75449112058
-
Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in
-
M.A. Ditzler, and M. Otyepka N.G. Walter Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in Acc. Chem. Res. 43 2010 40 47
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Walter, N.G.3
-
19
-
-
33748422686
-
The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation
-
DOI 10.1016/j.jmgm.2006.01.003, PII S1093326306000143
-
Y.G. Yingling, and B.A. Shapiro The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation J. Mol. Graph. Model 25 2006 261 274 (Pubitemid 44345278)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.2
, pp. 261-274
-
-
Yingling, Y.G.1
Shapiro, B.A.2
-
20
-
-
17844375121
-
Hinge-like motions in RNA Kink-turns: The role of the second A-minor motif and nominally unpaired bases
-
DOI 10.1529/biophysj.104.054916
-
F. Rázga, and J. Koca N.B. Leontis Hinge-like motions in RNA kink-turns: the role of the second A-minor motif and nominally unpaired bases Biophys. J. 88 2005 3466 3485 (Pubitemid 40586595)
-
(2005)
Biophysical Journal
, vol.88
, Issue.5
, pp. 3466-3485
-
-
Razga, F.1
Koca, J.2
Sponer, J.3
Leontis, N.B.4
-
21
-
-
1642458421
-
The kink-turn motif in RNA is dimorphic, and metal ion-dependent
-
DOI 10.1261/rna.5176604
-
T.A. Goody, and S.E. Melcher D.M. Lilley The kink-turn motif in RNA is dimorphic, and metal ion-dependent RNA 10 2004 254 264 (Pubitemid 38129830)
-
(2004)
RNA
, vol.10
, Issue.2
, pp. 254-264
-
-
Goody, T.A.1
Melcher, S.E.2
Norman, D.G.3
Lilley, D.M.J.4
-
22
-
-
17944388579
-
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets
-
DOI 10.1093/nar/gkg880
-
K. Réblová, and N. Spacková J. Sponer Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets Nucleic Acids Res. 31 2003 6942 6952 (Pubitemid 37508801)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.23
, pp. 6942-6952
-
-
Reblova, K.1
Spackova, N.2
Sponer, J.E.3
Koca, J.4
Sponer, J.5
-
23
-
-
80052451751
-
-
Reference deleted in proof.
-
Reference deleted in proof.
-
-
-
-
24
-
-
36849057065
-
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics
-
DOI 10.1529/biophysj.107.110056
-
K. Réblová, and E. Fadrná J. Sponer Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics Biophys. J. 93 2007 3932 3949 (Pubitemid 350223810)
-
(2007)
Biophysical Journal
, vol.93
, Issue.11
, pp. 3932-3949
-
-
Reblova, K.1
Fadrna, E.2
Sarzynska, J.3
Kulinski, T.4
Kulhanek, P.5
Ennifar, E.6
Koca, J.7
Sponer, J.8
-
25
-
-
67649363284
-
Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop
-
A.A. Chen, D.E. Draper, and R.V. Pappu Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop J. Mol. Biol. 390 2009 805 819
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 805-819
-
-
Chen, A.A.1
Draper, D.E.2
Pappu, R.V.3
-
26
-
-
0034662880
-
A retroviral RNA kissing complex containing only two G.C basepairs
-
C.H. Kim, and I. Tinoco Jr. A retroviral RNA kissing complex containing only two G.C basepairs Proc. Natl. Acad. Sci. USA 97 2000 9396 9401
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 9396-9401
-
-
Kim, C.H.1
Tinoco Jr., I.2
-
27
-
-
0034637111
-
The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
-
DOI 10.1126/science.289.5481.905
-
N. Ban, and P. Nissen T.A. Steitz The complete atomic structure of the large ribosomal subunit at 2.4 resolution Science 289 2000 905 920 (Pubitemid 30659939)
-
(2000)
Science
, vol.289
, Issue.5481
, pp. 905-920
-
-
Ban, N.1
Nissen, P.2
Hansen, J.3
Moore, P.B.4
Steitz, T.A.5
-
28
-
-
0035184520
-
Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site
-
DOI 10.1038/nsb727
-
E. Ennifar, and P. Walter P. Dumas Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site Nat. Struct. Biol. 8 2001 1064 1068 (Pubitemid 33101628)
-
(2001)
Nature Structural Biology
, vol.8
, Issue.12
, pp. 1064-1068
-
-
Ennifar, E.1
Walter, P.2
Ehresmann, B.3
Ehresmann, C.4
Dumas, P.5
-
29
-
-
80052427503
-
-
Reference deleted in proof.
-
Reference deleted in proof.
-
-
-
-
30
-
-
2942615089
-
The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
-
DOI 10.1016/j.jmb.2004.03.076, PII S0022283604003845
-
D.J. Klein, P.B. Moore, and T.A. Steitz The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit J. Mol. Biol. 340 2004 141 177 (Pubitemid 38739442)
-
(2004)
Journal of Molecular Biology
, vol.340
, Issue.1
, pp. 141-177
-
-
Klein, D.J.1
Moore, P.B.2
Steitz, T.A.3
-
32
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
T.E. Cheatham 3rd, P. Cieplak, and P.A. Kollman A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 16 1999 845 862 (Pubitemid 29157655)
-
(1999)
Journal of Biomolecular Structure and Dynamics
, vol.16
, Issue.4
, pp. 845-862
-
-
Cheatham III, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
33
-
-
0344796204
-
Ion water interaction potentials derived from free-energy perturbation simulations
-
J. Aqvist Ion water interaction potentials derived from free-energy perturbation simulations J. Phys. Chem. 94 1990 8021 8024
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8021-8024
-
-
Aqvist, J.1
-
35
-
-
0346366808
-
2+ Ion-binding Sites in the 5 S rRNA Loop e Inferred from Molecular Dynamics Simulations
-
DOI 10.1016/j.jmb.2003.10.057
-
2+ ion-binding sites in the 5S rRNA loop E inferred from molecular dynamics simulations J. Mol. Biol. 335 2004 555 571 (Pubitemid 37532656)
-
(2004)
Journal of Molecular Biology
, vol.335
, Issue.2
, pp. 555-571
-
-
Auffinger, P.1
Bielecki, L.2
Westhof, E.3
-
36
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W. Jorgensen, and J. Chandrasekhar M. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.1
Chandrasekhar, J.2
Klein, M.3
-
38
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
H. Berendsen, and J. Postma J. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.1
Postma, J.2
Haak, J.3
-
39
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J. Ryckaert, G. Ciccotti, and H. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.1
Ciccotti, G.2
Berendsen, H.3
-
41
-
-
77950228926
-
The sequence of HIV-1 TAR RNA helix controls cationic distribution
-
L. Sethaphong, and A. Singh Y.G. Yingling The sequence of HIV-1 TAR RNA helix controls cationic distribution J. Phys. Chem. C. 114 2010 5506 5512
-
(2010)
J. Phys. Chem. C.
, vol.114
, pp. 5506-5512
-
-
Sethaphong, L.1
Singh, A.2
Yingling, Y.G.3
-
42
-
-
33846479398
-
Hydration of alkali ions from first principles molecular dynamics revisited
-
T. Ikeda, M. Boero, and K. Terakura Hydration of alkali ions from first principles molecular dynamics revisited J. Chem. Phys. 126 2007 034501
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 034501
-
-
Ikeda, T.1
Boero, M.2
Terakura, K.3
-
43
-
-
33847142225
-
CAVER: A new tool to explore routes from protein clefts, pockets and cavities
-
M.O. Petřek, and P. Banáš J. Damborský CAVER: a new tool to explore routes from protein clefts, pockets and cavities BMC Bioinformatics 7 2006 316
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 316
-
-
Petřek, M.O.1
Banáš, P.2
Damborský, J.3
-
44
-
-
33847076903
-
Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles
-
DOI 10.1002/biot.200600208
-
J. Damborský, and M. Petrek M. Otyepka Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles Biotechnol. J. 2 2007 62 67 (Pubitemid 46744756)
-
(2007)
Biotechnology Journal
, vol.2
, Issue.1
, pp. 62-67
-
-
Damborsky, J.1
Petrek, M.2
Banas, P.3
Otyepka, M.4
-
46
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
DOI 10.1016/S0263-7855(97)00009-X, PII S026378559700009X
-
O.S. Smart, and J.G. Neduvelil M.S. Sansom HOLE: a program for the analysis of the pore dimensions of ion channel structural models J. Mol. Graph. 14 1996 354 360 376 (Pubitemid 27302826)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.6
, pp. 354-360
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.P.5
-
47
-
-
42449155819
-
RNA folding: Conformational statistics, folding kinetics, and ion electrostatics
-
S.J. Chen RNA folding: conformational statistics, folding kinetics, and ion electrostatics Annu Rev Biophys. 37 2008 197 214
-
(2008)
Annu Rev Biophys.
, vol.37
, pp. 197-214
-
-
Chen, S.J.1
-
48
-
-
77952896659
-
Compact intermediates in RNA folding
-
Woodson, S. A. Compact intermediates in RNA folding. Annu. Rev. Biophys. 39:61-77.
-
Annu. Rev. Biophys.
, vol.39
, pp. 61-77
-
-
Woodson, S.A.1
-
50
-
-
0038719800
-
A crystallographic study of the binding of 13 metal ions of two related RNA duplexes
-
DOI 10.1093/nar/gkg350
-
E. Ennifar, P. Walter, and P. Dumas A crystallographic study of the binding of 13 metal ions to two related RNA duplexes Nucleic Acids Res. 31 2003 2671 2682 (Pubitemid 37441752)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.10
, pp. 2671-2682
-
-
Ennifar, E.1
Walter, P.2
Dumas, P.3
-
51
-
-
33845563618
-
A third mode of DNA binding: Phosphate clamps by a polynuclear platinum complex
-
DOI 10.1021/ja062851y
-
S. Komeda, and T. Moulaei L.D. Williams A third mode of DNA binding: phosphate clamps by a polynuclear platinum complex J. Am. Chem. Soc. 128 2006 16092 16103 (Pubitemid 44936602)
-
(2006)
Journal of the American Chemical Society
, vol.128
, Issue.50
, pp. 16092-16103
-
-
Komeda, S.1
Moulaei, T.2
Woods, K.K.3
Chikuma, M.4
Farrell, N.P.5
Williams, L.D.6
-
52
-
-
0029379551
-
Let's get specific: The relationship between specificity and affinity
-
B.E. Eaton, L. Gold, and D.A. Zichi Let's get specific: the relationship between specificity and affinity Chem. Biol. 2 1995 633 638
-
(1995)
Chem. Biol.
, vol.2
, pp. 633-638
-
-
Eaton, B.E.1
Gold, L.2
Zichi, D.A.3
-
54
-
-
0011824888
-
Structures and energies of hydrogen-bonded DNA base pairs. A nonempirical study with inclusion of electron correlation
-
J. Sponer, J. Leszczynski, and P. Hobza Structures and energies of hydrogen-bonded DNA basepairs. A nonempirical study with inclusion of electron correlation J. Phys. Chem. 100 1996 1965 1974 (Pubitemid 126790022)
-
(1996)
Journal of Physical Chemistry
, vol.100
, Issue.5
, pp. 1965-1974
-
-
Sponer, J.1
Leszczynski, J.2
Hobza, P.3
-
55
-
-
0025267105
-
Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA i and RNA II
-
J. Tomizawa Control of ColE1 plasmid replication. Interaction of Rom protein with an unstable complex formed by RNA I and RNA II J. Mol. Biol. 212 1990 695 708
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 695-708
-
-
Tomizawa, J.1
|