-
1
-
-
12544255655
-
Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography
-
J. Benjamin, and B.K. Ganser-Pornillos G.J. Jensen Three-dimensional structure of HIV-1 virus-like particles by electron cryotomography J. Mol. Biol. 346 2005 577 588
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 577-588
-
-
Benjamin, J.1
Ganser-Pornillos, B.K.2
Jensen, G.J.3
-
2
-
-
33749462736
-
The structural and functional role of RNA in icosahedral virus assembly
-
DOI 10.1146/annurev.micro.60.080805.142304
-
A. Schneemann The structural and functional role of RNA in icosahedral virus assembly Annu. Rev. Microbiol. 60 2006 51 67 (Pubitemid 44627940)
-
(2006)
Annual Review of Microbiology
, vol.60
, pp. 51-67
-
-
Schneemann, A.1
-
3
-
-
33644873919
-
VIPERdb: A relational database for structural virology
-
C.M. Shepherd, and I.A. Borelli V.S. Reddy VIPERdb: a relational database for structural virology Nucleic Acids Res. 34 Database issue 2006 D386 D389
-
(2006)
Nucleic Acids Res.
, vol.34
, Issue.DATABASE ISSUE
-
-
Shepherd, C.M.1
Borelli, I.A.2
Reddy, V.S.3
-
4
-
-
37349114868
-
The Three-dimensional Structure of Genomic RNA in Bacteriophage MS2: Implications for Assembly
-
DOI 10.1016/j.jmb.2007.08.067, PII S0022283607011369
-
K. Toropova, and G. Basnak N.A. Ranson The three-dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly J. Mol. Biol. 375 2008 824 836 (Pubitemid 350297278)
-
(2008)
Journal of Molecular Biology
, vol.375
, Issue.3
, pp. 824-836
-
-
Toropova, K.1
Basnak, G.2
Twarock, R.3
Stockley, P.G.4
Ranson, N.A.5
-
5
-
-
0032549663
-
Refined structure of satellite tobacco mosaic virus at 1.8 A resolution
-
DOI 10.1006/jmbi.1997.1570
-
S.B. Larson, and J. Day A. McPherson Refined structure of satellite tobacco mosaic virus at 1.8 A resolution J. Mol. Biol. 277 1998 37 59 (Pubitemid 28151882)
-
(1998)
Journal of Molecular Biology
, vol.277
, Issue.1
, pp. 37-59
-
-
Larson, S.B.1
Day, J.2
Greenwood, A.3
Mcpherson, A.4
-
6
-
-
0027497651
-
Double-helical RNA in satellite tobacco mosaic virus
-
DOI 10.1038/361179a0
-
S.B. Larson, and S. Koszelak A. McPherson Double-helical RNA in satellite tobacco mosaic virus Nature 361 1993 179 182 (Pubitemid 23031356)
-
(1993)
Nature
, vol.361
, Issue.6408
, pp. 179-182
-
-
Larson, S.B.1
Koszelak, S.2
Day, J.3
Greenwood, A.4
Dodds, J.A.5
McPherson, A.6
-
7
-
-
0035252686
-
Satellite tobacco mosaic virus RNA: Structure and implications for assembly
-
DOI 10.1016/S0959-440X(00)00166-4
-
S.B. Larson, and A. McPherson Satellite tobacco mosaic virus RNA: structure and implications for assembly Curr. Opin. Struct. Biol. 11 2001 59 65 (Pubitemid 32155553)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.1
, pp. 59-65
-
-
Larson, S.B.1
McPherson, A.2
-
8
-
-
33644848399
-
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
-
DOI 10.1016/j.str.2005.11.014, PII S0969212606000608
-
P.L. Freddolino, and A.S. Arkhipov K. Schulten Molecular dynamics simulations of the complete satellite tobacco mosaic virus Structure 14 2006 437 449 (Pubitemid 43363477)
-
(2006)
Structure
, vol.14
, Issue.3
, pp. 437-449
-
-
Freddolino, P.L.1
Arkhipov, A.S.2
Larson, S.B.3
McPherson, A.4
Schulten, K.5
-
9
-
-
0027935972
-
Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs
-
A.P. Gultyaev, E. van Batenburg, and C.W.A. Pleij Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs J. Gen. Virol. 75 1994 2851 2856 (Pubitemid 24303208)
-
(1994)
Journal of General Virology
, vol.75
, Issue.10
, pp. 2851-2856
-
-
Gultyaev, A.P.1
Van Batenburg, E.2
Pleij, C.W.A.3
-
10
-
-
0027959313
-
A histidine accepting tRNA-like fold at the 3′-end of satellite tobacco mosaic virus RNA
-
B. Felden, and C. Florentz R. Giegé A histidine accepting tRNA-like fold at the 3′-end of satellite tobacco mosaic virus RNA Nucleic Acids Res. 22 1994 2882 2886
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2882-2886
-
-
Felden, B.1
Florentz, C.2
Giegé, R.3
-
11
-
-
0031572254
-
Structural analysis of a necrogenic strain of cucumber mosaic cucumovirus satellite RNA in planta
-
DOI 10.1006/viro.1997.8731
-
G. Rodriguez-Alvarado, and M.J. Roossinck Structural analysis of a necrogenic strain of cucumber mosaic cucumovirus satellite RNA in planta Virology 236 1997 155 166 (Pubitemid 27410363)
-
(1997)
Virology
, vol.236
, Issue.1
, pp. 155-166
-
-
Rodriguez-Alvarado, G.1
Roossinck, M.J.2
-
12
-
-
64249159586
-
Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution
-
A.C. Palmenberg, and D. Spiro S.B. Liggett Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution Science 324 2009 55 59
-
(2009)
Science
, vol.324
, pp. 55-59
-
-
Palmenberg, A.C.1
Spiro, D.2
Liggett, S.B.3
-
13
-
-
68449092202
-
Architecture and secondary structure of an entire HIV-1 RNA genome
-
J.M. Watts, and K.K. Dang K.M. Weeks Architecture and secondary structure of an entire HIV-1 RNA genome Nature 460 2009 711 716
-
(2009)
Nature
, vol.460
, pp. 711-716
-
-
Watts, J.M.1
Dang, K.K.2
Weeks, K.M.3
-
14
-
-
73849110514
-
Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain
-
C. Gherghe, and C.W. Leonard K.M. Weeks Secondary structure of the mature ex virio Moloney murine leukemia virus genomic RNA dimerization domain J. Virol. 84 2010 898 906
-
(2010)
J. Virol.
, vol.84
, pp. 898-906
-
-
Gherghe, C.1
Leonard, C.W.2
Weeks, K.M.3
-
15
-
-
78650628290
-
Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome
-
C. Gherghe, and T. Lombo K.M. Weeks Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome Proc. Natl. Acad. Sci. USA 107 2010 19248 19253
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 19248-19253
-
-
Gherghe, C.1
Lombo, T.2
Weeks, K.M.3
-
16
-
-
9144247039
-
First snapshots of the HIV-1 RNA structure in infected cells and in virions
-
DOI 10.1074/jbc.M408294200
-
J.-C. Paillart, and M. Dettenhofer R. Marquet First snapshots of the HIV-1 RNA structure in infected cells and in virions J. Biol. Chem. 279 2004 48397 48403 (Pubitemid 39540996)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.46
, pp. 48397-48403
-
-
Paillart, J.-C.1
Dettenhofer, M.2
Yu, X.-F.3
Ehresmann, C.4
Ehresmann, B.5
Marquet, R.6
-
17
-
-
0038176532
-
A novel long distance base-pairing interaction in human immunodeficiency virus type 1 rna occludes the gag start codon
-
DOI 10.1074/jbc.M210291200
-
T.E. Abbink, and B. Berkhout A novel long distance base-pairing interaction in human immunodeficiency virus type 1 RNA occludes the Gag start codon J. Biol. Chem. 278 2003 11601 11611 (Pubitemid 36792722)
-
(2003)
Journal of Biological Chemistry
, vol.278
, Issue.13
, pp. 11601-11611
-
-
Abbink, T.E.M.1
Berkhout, B.2
-
18
-
-
57449102624
-
Potential intra- and intermolecular interactions involving the unique-5′ region of the HIV-1 5′-UTR
-
S. Spriggs, and L. Garyu M.F. Summers Potential intra- and intermolecular interactions involving the unique-5′ region of the HIV-1 5′-UTR Biochemistry 47 2008 13064 13073
-
(2008)
Biochemistry
, vol.47
, pp. 13064-13073
-
-
Spriggs, S.1
Garyu, L.2
Summers, M.F.3
-
19
-
-
0037143493
-
Multiple secondary structure rearrangements during HIV-1 RNA dimerization
-
H. Huthoff, and B. Berkhout Multiple secondary structure rearrangements during HIV-1 RNA dimerization Biochemistry 41 2002 10439 10445
-
(2002)
Biochemistry
, vol.41
, pp. 10439-10445
-
-
Huthoff, H.1
Berkhout, B.2
-
20
-
-
34748833042
-
Effect of target secondary structure on RNAi efficiency
-
DOI 10.1261/rna.546207
-
Y. Shao, and C.Y. Chan Y. Ding Effect of target secondary structure on RNAi efficiency RNA 13 2007 1631 1640 (Pubitemid 47481671)
-
(2007)
RNA
, vol.13
, Issue.10
, pp. 1631-1640
-
-
Shao, Y.1
Chi, Y.C.2
Maliyekkel, A.3
Lawrence, C.E.4
Roninson, I.B.5
Ding, Y.6
-
21
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
DOI 10.1073/pnas.0401799101
-
D.H. Mathews, and M.D. Disney D.H. Turner Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure Proc. Natl. Acad. Sci. USA 101 2004 7287 7292 (Pubitemid 38638025)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.19
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
23
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
J.S. McCaskill The equilibrium partition function and base pair binding probabilities for RNA secondary structure Biopolymers 29 1990 1105 1119 (Pubitemid 20145703)
-
(1990)
Biopolymers
, vol.29
, Issue.6-7
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
24
-
-
0024477261
-
On findings all suboptimal foldings of an RNA molecule
-
M. Zuker On finding all suboptimal foldings of an RNA molecule Science 244 1989 48 52 (Pubitemid 19130742)
-
(1989)
Science
, vol.244
, Issue.4900
, pp. 48-52
-
-
Zuker, M.1
-
25
-
-
77952733078
-
Evaluation of the information content of RNA structure mapping data for secondary structure prediction
-
S. Quarrier, and J.S. Martin A. Laederach Evaluation of the information content of RNA structure mapping data for secondary structure prediction RNA 16 2010 1108 1117
-
(2010)
RNA
, vol.16
, pp. 1108-1117
-
-
Quarrier, S.1
Martin, J.S.2
Laederach, A.3
-
26
-
-
0346888665
-
A statistical sampling algorithm for RNA secondary structure prediction
-
DOI 10.1093/nar/gkg938
-
Y. Ding, and C.E. Lawrence A statistical sampling algorithm for RNA secondary structure prediction Nucleic Acids Res. 31 2003 7280 7301 (Pubitemid 38008457)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.24
, pp. 7280-7301
-
-
Ding, Y.1
Lawrence, C.E.2
-
27
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
DOI 10.1002/(SICI)1097-0282(199902)49:2<145::AID-BIP4>3.0.CO;2-G
-
S. Wuchty, and W. Fontana P. Schuster Complete suboptimal folding of RNA and the stability of secondary structures Biopolymers 49 1999 145 165 (Pubitemid 29061655)
-
(1999)
Biopolymers
, vol.49
, Issue.2
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
28
-
-
67449104206
-
Advances in RNA structure prediction from sequence: New tools for generating hypotheses about viral RNA structure-function relationships
-
S.J. Schroeder Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships J. Virol. 83 2009 6326 6334
-
(2009)
J. Virol.
, vol.83
, pp. 6326-6334
-
-
Schroeder, S.J.1
-
29
-
-
0016692310
-
Method for predicting RNA secondary structure
-
J.M. Pipas, and J.E. McMahon Method for predicting RNA secondary structure Proc. Natl. Acad. Sci. USA 72 1975 2017 2021
-
(1975)
Proc. Natl. Acad. Sci. USA
, vol.72
, pp. 2017-2021
-
-
Pipas, J.M.1
McMahon, J.E.2
-
30
-
-
57649129010
-
3′ terminal nucleotides determine thermodynamic stabilities of mismatches at the ends of RNA helices
-
K. Clanton-Arrowood, J. McGurk, and S.J. Schroeder 3′ terminal nucleotides determine thermodynamic stabilities of mismatches at the ends of RNA helices Biochemistry 47 2008 13418 13427
-
(2008)
Biochemistry
, vol.47
, pp. 13418-13427
-
-
Clanton-Arrowood, K.1
McGurk, J.2
Schroeder, S.J.3
-
31
-
-
34147193842
-
Stretching of homopolymeric RNA reveals single stranded helices and base-stacking
-
Y. Seol, and G.M. Skinner A. Halperin Stretching of homopolymeric RNA reveals single stranded helices and base-stacking Phys. Rev. Lett. 98 2007 158103 158107
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 158103-158107
-
-
Seol, Y.1
Skinner, G.M.2
Halperin, A.3
-
32
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
DOI 10.1006/jmbi.1999.2700
-
D.H. Mathews, and J. Sabina D.H. Turner Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288 1999 911 940 (Pubitemid 29248642)
-
(1999)
Journal of Molecular Biology
, vol.288
, Issue.5
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
33
-
-
0034622514
-
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA
-
DOI 10.1021/bi000229r
-
S.J. Schroeder, and D.H. Turner Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA Biochemistry 39 2000 9257 9274 (Pubitemid 30626318)
-
(2000)
Biochemistry
, vol.39
, Issue.31
, pp. 9257-9274
-
-
Schroeder, S.J.1
Turner, D.H.2
-
34
-
-
0000731487
-
The energetics of small internal loops in RNA
-
DOI 10.1002/1097-0282(1999)52:4<157::AID-BIP1001>3.0.CO;2-E
-
S.J. Schroeder, M.E. Burkard, and D.H. Turner The energetics of small internal loops in RNA Biopolymers 52 1999-2000 157 167 (Pubitemid 32472439)
-
(1999)
Biopolymers
, vol.52
, Issue.4
, pp. 157-167
-
-
Schroeder, S.J.1
Burkard, M.E.2
Turner, D.H.3
-
35
-
-
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
-
36
-
-
0035038089
-
Two alternating structures of the HIV-1 leader RNA
-
DOI 10.1017/S1355838201001881
-
H. Huthoff, and B. Berkhout Two alternating structures of the HIV-1 leader RNA RNA 7 2001 143 157 (Pubitemid 32381937)
-
(2001)
RNA
, vol.7
, Issue.1
, pp. 143-157
-
-
Huthoff, H.1
Berkhout, B.2
-
37
-
-
31144459945
-
Structural polymorphism of the HIV-1 leader region explored by computational methods
-
DOI 10.1093/nar/gki1015
-
W. Kasprzak, E. Bindewald, and B.A. Shapiro Structural polymorphism of the HIV-1 leader region explored by computational methods Nucleic Acids Res. 33 2005 7151 7163 (Pubitemid 43125083)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.22
, pp. 7151-7163
-
-
Kasprzak, W.1
Bindewald, E.2
Shapiro, B.A.3
-
38
-
-
3242877996
-
Sfold web server for statistical folding and rational design of nucleic acids
-
Y. Ding, C.Y. Chan, and C.E. Lawrence Sfold web server for statistical folding and rational design of nucleic acids Nucleic Acids Res. 32 Web Server issue 2004 W135 W141
-
(2004)
Nucleic Acids Res.
, vol.32
, Issue.WEB SERVER ISSUE
-
-
Ding, Y.1
Chan, C.Y.2
Lawrence, C.E.3
-
39
-
-
0026741428
-
Analysis of genetic heterogeneity within the type strain of satellite tobacco mosaic virus reveals variants and a strong bias for G to A substitution mutations
-
G. Kurath, M.E. Rey, and J.A. Dodds Analysis of genetic heterogeneity within the type strain of satellite tobacco mosaic virus reveals variants and a strong bias for G to A substitution mutations Virology 189 1992 233 244
-
(1992)
Virology
, vol.189
, pp. 233-244
-
-
Kurath, G.1
Rey, M.E.2
Dodds, J.A.3
-
40
-
-
0027296898
-
RNase protection analyses show high genetic diversity among field isolates of satellite tobacco mosaic virus
-
G. Kurath, J.A. Heick, and J.A. Dodds RNase protection analyses show high genetic diversity among field isolates of satellite tobacco mosaic virus Virology 194 1993 414 418
-
(1993)
Virology
, vol.194
, pp. 414-418
-
-
Kurath, G.1
Heick, J.A.2
Dodds, J.A.3
-
41
-
-
0029331365
-
Mutation analyses of molecularly cloned satellite tobacco mosaic virus during serial passage in plants: Evidence for hotspots of genetic change
-
G. Kurath, and J.A. Dodds Mutation analyses of molecularly cloned satellite tobacco mosaic virus during serial passage in plants: evidence for hotspots of genetic change RNA 1 1995 491 500
-
(1995)
RNA
, vol.1
, pp. 491-500
-
-
Kurath, G.1
Dodds, J.A.2
-
42
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
DOI 10.1093/nar/gkg595
-
M. Zuker Mfold web server for nucleic acid folding and hybridization prediction Nucleic Acids Res. 31 2003 3406 3415 (Pubitemid 37442169)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3406-3415
-
-
Zuker, M.1
-
43
-
-
0029061125
-
The computer simulation of RNA folding pathways using a genetic algorithm
-
A.P. Gultyaev, F.H. van Batenburg, and C.W. Pleij The computer simulation of RNA folding pathways using a genetic algorithm J. Mol. Biol. 250 1995 37 51
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 37-51
-
-
Gultyaev, A.P.1
Van Batenburg, F.H.2
Pleij, C.W.3
-
44
-
-
0043123153
-
Vienna RNA secondary structure server
-
DOI 10.1093/nar/gkg599
-
I.L. Hofacker Vienna RNA secondary structure server Nucleic Acids Res. 31 2003 3429 3431 (Pubitemid 37442172)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
45
-
-
33746320475
-
Revolutions in RNA secondary structure prediction
-
D.H. Mathews Revolutions in RNA secondary structure prediction J. Mol. Biol. 359 2006 526 532
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 526-532
-
-
Mathews, D.H.1
-
46
-
-
78649233212
-
Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy
-
N.J. Baird, and S.J. Ludtke T.R. Sosnick Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy J. Am. Chem. Soc. 132 2010 16352 16353
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 16352-16353
-
-
Baird, N.J.1
Ludtke, S.J.2
Sosnick, T.R.3
-
47
-
-
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 A 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
-
48
-
-
76249126156
-
Multiple native states reveal persistent ruggedness of an RNA folding landscape
-
S.V. Solomatin, and M. Greenfeld D. Herschlag Multiple native states reveal persistent ruggedness of an RNA folding landscape Nature 463 2010 681 684
-
(2010)
Nature
, vol.463
, pp. 681-684
-
-
Solomatin, S.V.1
Greenfeld, M.2
Herschlag, D.3
|