-
1
-
-
0029969687
-
Structural analysis of the interaction of the pyrimidine tract-binding protein with the internal ribosomal entry site of encephalomyocarditis virus and foot-and-mouth disease virus RNAs
-
Kolupaeva,V.G., Hellen,C.U. and Shatsky,I.N. (1996) Structural analysis of the interaction of the pyrimidine tract-binding protein with the internal ribosomal entry site of encephalomyocarditis virus and foot-and-mouth disease virus RNAs. RNA, 2, 1199-1212.
-
(1996)
RNA
, vol.2
, pp. 1199-1212
-
-
Hellen, C.U.1
Shatsky, I.N.2
-
2
-
-
0033623486
-
Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo
-
Lopez de Quinto,S. and Martinez-Salas,E. (2000) Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo. RNA, 6, 1380-1392.
-
(2000)
RNA
, vol.6
, pp. 1380-1392
-
-
Lopez De Quinto, S.1
Martinez-Salas, E.2
-
3
-
-
0034663980
-
A cell cycle-dependent protein serves as a template-specific translation initiation factor
-
Pilipenko,E.V., Pestova,T.V., Kolupaeva,V.G., Khitrina,E.V., Poperechnaya,A.N., Agol,V.I. and Hellen,C.U. (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev., 14, 2028-2045.
-
(2000)
Genes Dev.
, vol.14
, pp. 2028-2045
-
-
Agol, V.I.1
Hellen, C.U.2
-
4
-
-
0034852292
-
IRES interaction with translation initiation factors: Functional characterization of novel RNA contacts with eIF3, eIF4B, and eIF4GII
-
Lopez de Quinto,S., Lafuente,E. and Martinez-Salas,E. (2001) IRES interaction with translation initiation factors: functional characterization of novel RNA contacts with eIF3, eIF4B, and eIF4GII. RNA, 7, 1213-1226.
-
(2001)
RNA
, vol.7
, pp. 1213-1226
-
-
Lopez De Quinto, S.1
Lafuente, E.2
Martinez-Salas, E.3
-
5
-
-
0035040192
-
A novel protein-RNA binding assay: Functional interactions of the foot-and-mouth disease virus internal ribosome entry site with cellular proteins
-
Stassinopoulos,I.A. and Belsham,G.J. (2001) A novel protein-RNA binding assay: functional interactions of the foot-and-mouth disease virus internal ribosome entry site with cellular proteins. RNA, 7, 114-122.
-
(2001)
RNA
, vol.7
, pp. 114-122
-
-
Stassinopoulos, I.A.1
Belsham, G.J.2
-
6
-
-
34447530523
-
Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA
-
Andreev,D.E., Fernandez-Miragall,O., Ramajo,J., Dmitriev,S.E., Terenin,I.M., Martinez-Salas,E. and Shatsky,I.N. (2007) Differential factor requirement to assemble translation initiation complexes at the alternative start codons of foot-and-mouth disease virus RNA. RNA, 13, 1366-1374.
-
(2007)
RNA
, vol.13
, pp. 1366-1374
-
-
Martinez-Salas, E.1
Shatsky, I.N.2
-
7
-
-
59649126267
-
A novel role for Gemin5 in mRNA translation
-
Pacheco,A., Lopez de Quinto,S., Ramajo,J., Fernandez,N. and Martinez-Salas,E. (2009) A novel role for Gemin5 in mRNA translation. Nucleic Acids Res., 37, 582-590.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 582-590
-
-
Ramajo, J.1
Fernandez, N.2
Martinez-Salas, E.3
-
8
-
-
0030999946
-
Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation
-
Lopez de Quinto,S. and Martinez-Salas,E. (1997) Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. J. Virol., 71, 4171-4175.
-
(1997)
J. Virol.
, vol.71
, pp. 4171-4175
-
-
Lopez De Quinto, S.1
Martinez-Salas, E.2
-
9
-
-
31044449305
-
Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation
-
Fernandez-Miragall,O., Ramos,R., Ramajo,J. and Martinez-Salas,E. (2006) Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA, 12, 223-234.
-
(2006)
RNA
, vol.12
, pp. 223-234
-
-
Ramajo, J.1
Martinez-Salas, E.2
-
10
-
-
80455168337
-
Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation
-
Fernandez,N., Fernandez-Miragall,O., Ramajo,J., Garcia-Sacristan,A., Bellora,N., Eyras,E., Briones,C. and Martinez-Salas,E. (2011) Structural basis for the biological relevance of the invariant apical stem in IRES-mediated translation. Nucleic Acids Res., 39, 8572-8585.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 8572-8585
-
-
Briones, C.1
Martinez-Salas, E.2
-
11
-
-
78650261546
-
Structural analysis provides insights into the modular organization of picornavirus IRES
-
Fernandez,N., Garcia-Sacristan,A., Ramajo,J., Briones,C. and Martinez-Salas,E. (2011) Structural analysis provides insights into the modular organization of picornavirus IRES. Virology, 409, 251-261.
-
(2011)
Virology
, vol.409
, pp. 251-261
-
-
Briones, C.1
Martinez-Salas, E.2
-
12
-
-
0037370110
-
Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution
-
Correll,C.C. and Swinger,K. (2003) Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4 A resolution. RNA, 9, 355-363.
-
(2003)
RNA
, vol.9
, pp. 355-363
-
-
Correll, C.C.1
Swinger, K.2
-
13
-
-
10744229009
-
Structural organization of a viral IRES depends on the integrity of the GNRA motif
-
Fernandez-Miragall,O. and Martinez-Salas,E. (2003) Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA, 9, 1333-1344.
-
(2003)
RNA
, vol.9
, pp. 1333-1344
-
-
Fernandez-Miragall, O.1
Martinez-Salas, E.2
-
14
-
-
2442457098
-
NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: A single C to U substitution drastically changes the shape and flexibility of RNA
-
Du,Z., Ulyanov,N.B., Yu,J., Andino,R. and James,T.L. (2004) NMR structures of loop B RNAs from the stem-loop IV domain of the enterovirus internal ribosome entry site: a single C to U substitution drastically changes the shape and flexibility of RNA. Biochemistry, 43, 5757-5771.
-
(2004)
Biochemistry
, vol.43
, pp. 5757-5771
-
-
Andino, R.1
James, T.L.2
-
15
-
-
0032863246
-
A selection system for functional internal ribosome entry site (IRES) elements: Analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES
-
Robertson,M.E., Seamons,R.A. and Belsham,G.J. (1999) A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES. RNA, 5, 1167-1179.
-
(1999)
RNA
, vol.5
, pp. 1167-1179
-
-
Seamons, R.A.1
Belsham, G.J.2
-
16
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Zuker, M.1
Turner, D.H.2
-
17
-
-
0029050831
-
A nomenclature of junctions and branchpoints in nucleic acids
-
Lilley,D.M., Clegg,R.M., Diekmann,S., Seeman,N.C., Von Kitzing,E. and Hagerman,P.J. (1995) A nomenclature of junctions and branchpoints in nucleic acids. Nucleic Acids Res., 23, 3363-3364.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 3363-3364
-
-
Von Kitzing, E.1
Hagerman, P.J.2
-
18
-
-
0036237981
-
Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation
-
Kieft,J.S., Zhou,K., Grech,A., Jubin,R. and Doudna,J.A. (2002) Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struct. Biol., 9, 370-374.
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 370-374
-
-
Jubin, R.1
Doudna, J.A.2
-
19
-
-
74249115345
-
Topology links RNA secondary structure with global conformation, dynamics, and adaptation
-
Bailor,M.H., Sun,X. and Al-Hashimi,H.M. (2010) Topology links RNA secondary structure with global conformation, dynamics, and adaptation. Science, 327, 202-206.
-
(2010)
Science
, vol.327
, pp. 202-206
-
-
Sun, X.1
Al-Hashimi, H.M.2
-
20
-
-
70349238567
-
Tertiary motifs revealed in analyses of higher-order RNA junctions
-
Laing,C., Jung,S., Iqbal,A. and Schlick,T. (2009) Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol., 393, 67-82.
-
(2009)
J. Mol. Biol.
, vol.393
, pp. 67-82
-
-
Iqbal, A.1
Schlick, T.2
-
21
-
-
67449103067
-
Analysis of four-way junctions in RNA structures
-
Laing,C. and Schlick,T. (2009) Analysis of four-way junctions in RNA structures. J. Mol. Biol., 390, 547-559.
-
(2009)
J. Mol. Biol.
, vol.390
, pp. 547-559
-
-
Laing, C.1
Schlick, T.2
-
22
-
-
29844453234
-
Topology of three-way junctions in folded RNAs
-
Lescoute,A. and Westhof,E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
-
(2006)
RNA
, vol.12
, pp. 83-93
-
-
Lescoute, A.1
Westhof, E.2
-
23
-
-
0016362013
-
The general structure of transfer RNA molecules
-
Kim,S.H., Sussman,J.L., Suddath,F.L., Quigley,G.J., McPherson,A., Wang,A.H., Seeman,N.C. and Rich,A. (1974) The general structure of transfer RNA molecules. Proc. Natl Acad. Sci. USA, 71, 4970-4974.
-
(1974)
Proc. Natl Acad. Sci. USA
, vol.71
, pp. 4970-4974
-
-
Seeman, N.C.1
Rich, A.2
-
24
-
-
0029820625
-
Crystal structure of a group i ribozyme domain: Principles of RNA packing
-
Cate,J.H., Gooding,A.R., Podell,E., Zhou,K., Golden,B.L., Kundrot,C.E., Cech,T.R. and Doudna,J.A. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science, 273, 1678-1685.
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
Cech, T.R.1
Doudna, J.A.2
-
25
-
-
79958073354
-
Computational approaches to RNA structure prediction, analysis, and design
-
Laing,C. and Schlick,T. (2011) Computational approaches to RNA structure prediction, analysis, and design. Curr. Opin. Struct. Biol., 21, 306-318.
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 306-318
-
-
Laing, C.1
Schlick, T.2
-
26
-
-
77953784130
-
Computational approaches to 3D modeling of RNA
-
Laing,C. and Schlick,T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens. Matter, 22, 283101.
-
(2010)
J. Phys. Condens. Matter
, vol.22
, pp. 283101
-
-
Laing, C.1
Schlick, T.2
-
27
-
-
84862969708
-
Predicting coaxial helical stacking in RNA junctions
-
Laing,C., Wen,D., Wang,J.T. and Schlick,T. (2011) Predicting coaxial helical stacking in RNA junctions. Nucleic Acids Res., 40, 487-498.
-
(2011)
Nucleic Acids Res.
, vol.40
, pp. 487-498
-
-
Wang, J.T.1
Schlick, T.2
-
28
-
-
0024355303
-
Conservation of the secondary structure elements of the 50-untranslated region of cardio- and aphthovirus RNAs
-
Pilipenko,E.V., Blinov,V.M., Chernov,B.K., Dmitrieva,T.M. and Agol,V.I. (1989) Conservation of the secondary structure elements of the 50-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res., 17, 5701-5711.
-
(1989)
Nucleic Acids Res.
, vol.17
, pp. 5701-5711
-
-
Dmitrieva, T.M.1
Agol, V.I.2
-
29
-
-
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
-
30
-
-
25444439861
-
GenBank
-
Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Sayers,E.W. (2011) GenBank. Nucleic Acids Res., 39, D32-D37.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Ostell, J.1
Sayers, E.W.2
-
31
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin,M.A., Blackshields,G., Brown,N.P., Chenna,R., McGettigan,P.A., McWilliam,H., Valentin,F., Wallace,I.M., Wilm,A., Lopez,R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Lopez, R.1
-
32
-
-
48449084852
-
RNALogo: A new approach to display structural RNA alignment
-
Chang,T.H., Horng,J.T. and Huang,H.D. (2008) RNALogo: a new approach to display structural RNA alignment. Nucleic Acids Res., 36, W91-W96.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Horng, J.T.1
Huang, H.D.2
-
33
-
-
0035478854
-
Random forests
-
Breiman,L. (2001) Random forests. Mach. Learn., 45, 5-32.
-
(2001)
Mach. Learn.
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
34
-
-
58249111738
-
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
-
Jonikas,M.A., Radmer,R.J., Laederach,A., Das,R., Pearlman,S., Herschlag,D. and Altman,R.B. (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
-
-
Herschlag, D.1
Altman, R.B.2
-
35
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E. 3rd, Laughton,C.A. and Orozco,M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
-
(2007)
Biophys. J.
, vol.92
, pp. 3817-3829
-
-
Cheatham Iii, T.E.1
Laughton, C.A.2
Orozco, M.3
-
36
-
-
0029011701
-
A second generation force field for the simulation of proteins nucleic acids, and organic molecules
-
Cornell,W.D., Cieplak,P., Bayly,C.I., Gould,I.R., Merz,K.M., Ferguson,D.M., Spellmeyer,D.C., Fox,T., Caldwell,J.W. and Kollman,P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, pp. 5179-5197
-
-
Caldwell, J.W.1
Kollman, P.A.2
-
37
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips,J.C., Braun,R., Wang,W., Gumbart,J., Tajkhorshid,E., Villa,E., Chipot,C., Skeel,R.D., Kale,L. and Schulten,K. (2005) Scalable molecular dynamics with NAMD. J. Comput. Chem., 26, 1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Kale, L.1
Schulten, K.2
-
38
-
-
77952472539
-
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H++ forms are most consistent with crystal structures of hairpin ribozyme
-
Mlynsky,V., Banas,P., Hollas,D., Reblova,K., Walter,N.G., Sponer,J. and Otyepka,M. (2010) Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H++ forms are most consistent with crystal structures of hairpin ribozyme. J. Phys. Chem. B, 114, 6642-6652.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 6642-6652
-
-
Mlynsky, V.1
Banas, P.2
Hollas, D.3
Reblova, K.4
Walter, N.G.5
Sponer, J.6
Otyepka, M.7
-
39
-
-
84864479919
-
Structure and mechanical properties of the ribosomal L1 stalk three-way junction
-
Reblova,K., Sponer,J. and Lankas,F. (2012) Structure and mechanical properties of the ribosomal L1 stalk three-way junction. Nucleic Acids Res., 40, 6290-6303.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 6290-6303
-
-
Reblova, K.1
Sponer, J.2
Lankas, F.3
-
40
-
-
80052820313
-
Refinement of the Cornell et al nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
-
Zgarbova,M., Otyepka,M., Sponer,J., Mladek,A., Banas,P., Cheatham,T.E. 3rd and Jurecka,P. (2011) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J. Chem. Theory Comput., 7, 2886-2902.
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2886-2902
-
-
Zgarbova, M.1
Otyepka, M.2
Sponer, J.3
Mladek, A.4
Banas, P.5
Cheatham Iii, T.E.6
Jurecka, P.7
-
41
-
-
84855656902
-
Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs
-
Yildirim,I., Kennedy,S.D., Stern,H.A., Hart,J.M., Kierzek,R. and Turner,D.H. (2012) Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs. J. Chem. Theory Comput., 8, 172-181.
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 172-181
-
-
Yildirim, I.1
Kennedy, S.D.2
Stern, H.A.3
Hart, J.M.4
Kierzek, R.5
Turner, D.H.6
-
42
-
-
79959292152
-
ModeRNA: A tool for comparative modeling of RNA 3D structure
-
Rother,M., Rother,K., Puton,T. and Bujnicki,J.M. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 4007-4022
-
-
Rother, M.1
Rother, K.2
Puton, T.3
Bujnicki, J.M.4
-
43
-
-
0023462809
-
Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena
-
Kim,S.H. and Cech,T.R. (1987) Three-dimensional model of the active site of the self-splicing rRNA precursor of Tetrahymena. Proc. Natl Acad. Sci. USA, 84, 8788-8792.
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 8788-8792
-
-
Kim, S.H.1
Cech, T.R.2
-
44
-
-
0030959348
-
Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: Comparison with in vivo evolution
-
Costa,M. and Michel,F. (1997) Rules for RNA recognition of GNRA tetraloops deduced by in vitro selection: comparison with in vivo evolution. EMBO J., 16, 3289-3302.
-
(1997)
EMBO J.
, vol.16
, pp. 3289-3302
-
-
Costa, M.1
Michel, F.2
-
45
-
-
80053207214
-
In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses
-
Burks,J.M., Zwieb,C., Muller,F., Wower,I.K. and Wower,J. (2011) In silico analysis of IRES RNAs of foot-and-mouth disease virus and related picornaviruses. Arch. Virol., 156, 1737-1747.
-
(2011)
Arch. Virol.
, vol.156
, pp. 1737-1747
-
-
Wower, I.K.1
Wower, J.2
-
46
-
-
79956058665
-
Biomolecularmodeling and simulation: A field coming of age
-
Schlick,T., Collepardo-Guevara,R., Halvorsen,L.A., Jung,S. and Xiao,X. (2011) Biomolecularmodeling and simulation: a field coming of age. Q. Rev. Biophys., 44, 191-228.
-
(2011)
Q. Rev. Biophys.
, vol.44
, pp. 191-228
-
-
Jung, S.1
Xiao, X.2
-
47
-
-
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
-
48
-
-
42749086185
-
The impact of RNA structure on picornavirus IRES activity
-
Martinez-Salas,E. (2008) The impact of RNA structure on picornavirus IRES activity. Trends Microbiol., 16, 230-237.
-
(2008)
Trends Microbiol.
, vol.16
, pp. 230-237
-
-
Martinez-Salas, E.1
-
49
-
-
0344980095
-
Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES
-
Ramos,R. and Martinez-Salas,E. (1999) Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES). RNA, 5, 1374-1383.
-
(1999)
RNA
, vol.5
, pp. 1374-1383
-
-
Ramos, R.1
Martinez-Salas, E.2
-
50
-
-
34249103881
-
Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element
-
Serrano,P., Gomez,J. and Martinez-Salas,E. (2007) Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element. RNA, 13, 849-859.
-
(2007)
RNA
, vol.13
, pp. 849-859
-
-
Gomez, J.1
Martinez-Salas, E.2
-
51
-
-
33847318371
-
Molecular dynamics simulations of RNA: An in silico single molecule approach
-
McDowell,S.E., Spackova,N., Sponer,J. and Walter,N.G. (2007) Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers, 85, 169-184.
-
(2007)
Biopolymers
, vol.85
, pp. 169-184
-
-
Sponer, J.1
Walter, N.G.2
-
52
-
-
0345631645
-
Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations
-
Sponer,J., Burda,J.M.S., Leszczynski,J. and Hobza,P. (1998) Interaction between the guanine-cytosine Watson-Crick DNA base pair and hydrated group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and group IIb (Zn2+, Cd2+, Hg2+) metal cations. J. Phys. Chem. A, 102, 5951-5957.
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5951-5957
-
-
Sponer, J.1
Burda, J.M.S.2
Leszczynski, J.3
Hobza, P.4
-
53
-
-
33746388359
-
Structure, dynamics, and elasticity of free 16 s rRNA helix 44 studied by molecular dynamics simulations
-
Reblova,K., Lankas,F., Razga,F., Krasovska,M.V., Koca,J. and Sponer,J. (2006) Structure, dynamics, and elasticity of free 16 s rRNA helix 44 studied by molecular dynamics simulations. Biopolymers, 82, 504-520.
-
(2006)
Biopolymers
, vol.82
, pp. 504-520
-
-
Koca, J.1
Sponer, J.2
-
54
-
-
17844375121
-
Hinge-like motions in RNA kink-turns: The role of the second a-minor motif and nominally unpaired bases
-
Razga,F., Koca,J., Sponer,J. and Leontis,N.B. (2005) Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases. Biophys. J., 88, 3466-3485.
-
(2005)
Biophys. J.
, vol.88
, pp. 3466-3485
-
-
Razga, F.1
Koca, J.2
Sponer, J.3
Leontis, N.B.4
-
55
-
-
0029878720
-
VMD: Visual molecular dynamics
-
Humphrey,W., Dalke,A. and Schulten,K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 27-38.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 27-38
-
-
Dalke, A.1
Schulten, K.2
-
56
-
-
27344454932
-
GROMACS: Fast flexible, and free
-
Van Der Spoel,D., Lindahl,E., Hess,B., Groenhof,G., Mark,A.E. and Berendsen,H.J. (2005) GROMACS: fast, flexible, and free. J. Comput. Chem., 26, 1701-1718.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
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