-
1
-
-
12844260994
-
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
-
Bai, Y., Das, R., Millett, I.S., Herschlag, D., & Doniach, S. (2005). Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proceedings of the National Academy of Sciences, 102, 1035-1040.
-
(2005)
Proceedings of the National Academy of Sciences
, vol.102
, pp. 1035-1040
-
-
Bai, Y.1
Das, R.2
Millett, I.S.3
Herschlag, D.4
Doniach, S.5
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., Gunsteren, W.F.V., DiNola, A., & Haak, J.R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics, 81, 3684-3690.
-
(1984)
Journal of Chemical Physics
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Gunsteren, W.F.V.3
Dinola, A.4
Haak, J.R.5
-
3
-
-
0029796006
-
Role of the DIS hairpin in replication of human immunodeficiency virus type 1
-
Berkhout, B., & van Wamel, J.L. (1996). Role of the DIS hairpin in replication of human immunodeficiency virus type 1. Journal of Virology, 70, 723-6732.
-
(1996)
Journal of Virology
, vol.70
, pp. 723-6732
-
-
Berkhout, B.1
Van Wamel, J.L.2
-
4
-
-
58049201323
-
-
San Francisco, CA: University of California
-
Case, D.A., Darden, T.A., Cheatham, T.E.III, Simmerling, C.L., Wang, J., Duke, R.E., ...Kollman, P.A. (2008). AMBER 10. San Francisco, CA: University of California.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham Iii, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Kollman, P.A.7
-
5
-
-
0032922174
-
A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
-
Cheatham, T.E.III, Cieplak, P., & Kollman, P.A. (1999). A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. Journal of Biomolecular Structure & Dynamics, 16, 845-862.
-
(1999)
Journal of Biomolecular Structure & Dynamics
, vol.16
, pp. 845-862
-
-
Cheatham Iii, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
6
-
-
10844257474
-
Building programmable jigsaw puzzles with RNA
-
Chworos, A., Severcan, I., Koyfman, A.Y., Weinkam, P., Oroudjev, E., Hansma, H.G., & Jaeger, L. (2004). Building programmable jigsaw puzzles with RNA. Science, 306, 2068-2072.
-
(2004)
Science
, vol.306
, pp. 2068-2072
-
-
Chworos, A.1
Severcan, I.2
Koyfman, A.Y.3
Weinkam, P.4
Oroudjev, E.5
Hansma, H.G.6
Jaeger, L.7
-
7
-
-
9444271764
-
Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA
-
Clever, J.L., Wong, M.L., & Parslow, T.G. (1996). Requirements for kissing-loop-mediated dimerization of human immunodeficiency virus RNA. Journal of Virology, 70, 5902-5908.
-
(1996)
Journal of Virology
, vol.70
, pp. 5902-5908
-
-
Clever, J.L.1
Wong, M.L.2
Parslow, T.G.3
-
8
-
-
31344481887
-
Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies
-
Ennifar, E., & Dumas, P. (2006). Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies. Journal of Molecular Biology, 356, 771-782.
-
(2006)
Journal of Molecular Biology
, vol.356
, pp. 771-782
-
-
Ennifar, E.1
Dumas, P.2
-
9
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H., & Pedersen, L.G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103, 8577-8593.
-
(1995)
Journal of Chemical Physics
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
10
-
-
0033066713
-
Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex
-
Girard, F., Barbault, F., Gouyette, C., Huynh-Dinh, T., Paoletti, J., & Lancelot, G. (1999). Dimer initiation sequence of HIV-1Lai genomic RNA: NMR solution structure of the extended duplex. Journal of Biomolecular Structure & Dynamics, 16, 1145-1157.
-
(1999)
Journal of Biomolecular Structure & Dynamics
, vol.16
, pp. 1145-1157
-
-
Girard, F.1
Barbault, F.2
Gouyette, C.3
Huynh-Dinh, T.4
Paoletti, J.5
Lancelot, G.6
-
11
-
-
79851470025
-
Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes
-
Grabow, W.W., Zakrevsky, P., Afonin, K.A., Chworos, A., Shapiro, B.A., & Jaeger, L. (2011). Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. Nano Letters, 11, 878-887.
-
(2011)
Nano Letters
, vol.11
, pp. 878-887
-
-
Grabow, W.W.1
Zakrevsky, P.2
Afonin, K.A.3
Chworos, A.4
Shapiro, B.A.5
Jaeger, L.6
-
12
-
-
0029900161
-
Evidence that a kissing loop structure facilitates genomic RNA dimerization inHIV-1
-
Haddrick, M., Lear, A.L., Cann, A.J., & Heaphy, S. (1996). Evidence that a kissing loop structure facilitates genomic RNA dimerization inHIV-1. Journal of Molecular Biology, 259, 58-68.
-
(1996)
Journal of Molecular Biology
, vol.259
, pp. 58-68
-
-
Haddrick, M.1
Lear, A.L.2
Cann, A.J.3
Heaphy, S.4
-
13
-
-
0346341029
-
TectoRNA and ′kissing-loop′ RNA: Atomic force microscopy of self-assembling RNA structures
-
Hansma, H.G., Oroudjev, E., Baudrey, S., & Jaeger, L. (2003). TectoRNA and ′kissing-loop′ RNA: Atomic force microscopy of self-assembling RNA structures. Journal of Microscopy, 212, 273-279.
-
(2003)
Journal of Microscopy
, vol.212
, pp. 273-279
-
-
Hansma, H.G.1
Oroudjev, E.2
Baudrey, S.3
Jaeger, L.4
-
14
-
-
59649095963
-
A short guide for molecular dynamics simulations of RNA systems
-
Hashem, Y., & Auffinger, P. (2009). A short guide for molecular dynamics simulations of RNA systems. Methods, 47, 187-197.
-
(2009)
Methods
, vol.47
, pp. 187-197
-
-
Hashem, Y.1
Auffinger, P.2
-
15
-
-
0035863772
-
TectoRNA: Modular assembly units for the construction of RNA nanoobjects
-
Jaeger, L., Westhof, E., & Leontis, N.B. (2001). TectoRNA: Modular assembly units for the construction of RNA nanoobjects. Nucleic Acids Research, 29, 455-463.
-
(2001)
Nucleic Acids Research
, vol.29
, pp. 455-463
-
-
Jaeger, L.1
Westhof, E.2
Leontis, N.B.3
-
16
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. Journal of Chemical Physics, 79, 926-935.
-
(1983)
Journal of Chemical Physics
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Klein, M.L.4
-
17
-
-
0032827805
-
Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding
-
Jossinet, F., Paillart, J.C., Westhof, E., Hermann, T., Skripkin, E., Lodmell, J.S., ...Marquet, R. (1999). Dimerization of HIV-1 genomic RNA of subtypes A and B: RNA loop structure and magnesium binding. RNA, 5, 1222-1234.
-
(1999)
RNA
, vol.5
, pp. 1222-1234
-
-
Jossinet, F.1
Paillart, J.C.2
Westhof, E.3
Hermann, T.4
Skripkin, E.5
Lodmell, J.S.6
Marquet, R.7
-
18
-
-
79958738880
-
Use of RNA structure flexibility data in nanostructure modeling
-
Kasprzak, W., Bindewald, E., Kim, T., Jaeger, L., & Shapiro, B.A. (2011). Use of RNA structure flexibility data in nanostructure modeling. Methods, 54, 239-250.
-
(2011)
Methods
, vol.54
, pp. 239-250
-
-
Kasprzak, W.1
Bindewald, E.2
Kim, T.3
Jaeger, L.4
Shapiro, B.A.5
-
19
-
-
0036975258
-
HIV-1Lai genomic RNA: Combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin
-
Kieken, F., Arnoult, E., Barbault, F., Paquet, F., Huynh-Dinh, T., Paoletti, J., ...Lancelot, F. (2002). HIV-1Lai genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin. European Biophysics Journal, 31, 521-531.
-
(2002)
European Biophysics Journal
, vol.31
, pp. 521-531
-
-
Kieken, F.1
Arnoult, E.2
Barbault, F.3
Paquet, F.4
Huynh-Dinh, T.5
Paoletti, J.6
Lancelot, F.7
-
20
-
-
31544475991
-
A new NMR solution structure of the SL1 HIV-1 (Lai) loop-loop dimer
-
Kieken, F., Paquet, F., Brule, F., Paoletti, J., & Lancelot, G. (2006). A new NMR solution structure of the SL1 HIV-1 (Lai) loop-loop dimer. Nucleic Acids Research, 34, 343-352.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 343-352
-
-
Kieken, F.1
Paquet, F.2
Brule, F.3
Paoletti, J.4
Lancelot, G.5
-
21
-
-
79751526262
-
Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign
-
Kim, T., Marquez, V.E., Barchi, J.J.Jr., & Shapiro, B.A. (2011). Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign. Journal of Molecular Graphics and Modelling, 29, 624-634.
-
(2011)
Journal of Molecular Graphics and Modelling
, vol.29
, pp. 624-634
-
-
Kim, T.1
Marquez, V.E.2
Barchi, J.J.Jr.3
Shapiro, B.A.4
-
22
-
-
24144470073
-
Controlled spacing of cationic gold nanoparticles by nanocrown RNA
-
Koyfman, A.Y., Braun, G., Magonov, S., Chworos, A., Reich, N.O., & Jaeger, L. (2005). Controlled spacing of cationic gold nanoparticles by nanocrown RNA. Journal of the American Chemical Society, 127, 11886-11887.
-
(2005)
Journal of the American Chemical Society
, vol.127
, pp. 11886-11887
-
-
Koyfman, A.Y.1
Braun, G.2
Magonov, S.3
Chworos, A.4
Reich, N.O.5
Jaeger, L.6
-
23
-
-
0028027708
-
A 19-nucleotide sequence upstream of the 59 major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA
-
Laughrea, M., & Jette, L. (1994). A 19-nucleotide sequence upstream of the 59 major splice donor is part of the dimerization domain of human immunodeficiency virus 1 genomic RNA. Biochemistry, 33, 13464-13474.
-
(1994)
Biochemistry
, vol.33
, pp. 13464-13474
-
-
Laughrea, M.1
Jette, L.2
-
24
-
-
0030019828
-
Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation
-
Laughrea, M., & Jette, L. (1996). Kissing-loop model of HIV-1 genome dimerization: HIV-1 RNAs can assume alternative dimeric forms, and all sequences upstream or downstream of hairpin 248-271 are dispensable for dimer formation. Biochemistry, 35, 1589-1598.
-
(1996)
Biochemistry
, vol.35
, pp. 1589-1598
-
-
Laughrea, M.1
Jette, L.2
-
25
-
-
0033827659
-
Convergence of natural and artificial evolution on an RNA loop-loop interaction: The HIV-1 dimerization initiation site
-
Lodmell, J.S., Ehresmann, C., Ehresmann, B., & Marquet, R. (2000). Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site. RNA, 6, 1267-1276.
-
(2000)
RNA
, vol.6
, pp. 1267-1276
-
-
Lodmell, J.S.1
Ehresmann, C.2
Ehresmann, B.3
Marquet, R.4
-
26
-
-
0032413255
-
Oligonucleotide-mediated inhibition of genomic RNA dimerization of HIV-1 strains MAL and LAI: A comparative analysis
-
Lodmell, J.S., Paillart, J.C., Mignot, D., Ehresmann, B., Ehresmann, C., & Marquet, R. (1998). Oligonucleotide-mediated inhibition of genomic RNA dimerization of HIV-1 strains MAL and LAI: A comparative analysis. Antisense and Nucleic Acid Drug Development, 8, 517-529.
-
(1998)
Antisense and Nucleic Acid Drug Development
, vol.8
, pp. 517-529
-
-
Lodmell, J.S.1
Paillart, J.C.2
Mignot, D.3
Ehresmann, B.4
Ehresmann, C.5
Marquet, R.6
-
27
-
-
31544436952
-
Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo
-
Lorenz, C., Piganeau, N., & Schroeder, R. (2006). Stabilities of HIV-1 DIS type RNA loop-loop interactions in vitro and in vivo. Nucleic Acids Research, 34, 334-342.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 334-342
-
-
Lorenz, C.1
Piganeau, N.2
Schroeder, R.3
-
29
-
-
0029868164
-
A kissing complex together with a stable dimer is involved in the HIV- 1Lai RNA dimerization process in vitro
-
Muriaux, D., Fosse, P., & Paoletti, J. (1996). A kissing complex together with a stable dimer is involved in the HIV- 1Lai RNA dimerization process in vitro. Biochemistry, 35, 5075-5082.
-
(1996)
Biochemistry
, vol.35
, pp. 5075-5082
-
-
Muriaux, D.1
Fosse, P.2
Paoletti, J.3
-
30
-
-
0028986869
-
Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 59 leader region is evidenced by an antisense oligonucleotide
-
Muriaux, D., Girard, P.M., Bonnet-Mathoniere, B., & Paoletti, J. (1995). Dimerization of HIV-1Lai RNA at low ionic strength. An autocomplementary sequence in the 59 leader region is evidenced by an antisense oligonucleotide. Journal of Biological Chemistry, 270, 8209-8216.
-
(1995)
Journal of Biological Chemistry
, vol.270
, pp. 8209-8216
-
-
Muriaux, D.1
Girard, P.M.2
Bonnet-Mathoniere, B.3
Paoletti, J.4
-
31
-
-
0030480326
-
NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer
-
Muriaux, D., Rocquigny, H. De., Roques, B.P., & Paoletti, J. (1996). NCp7 activates HIV-1Lai RNA dimerization by converting a transient loop-loop complex into a stable dimer. Journal of Biological Chemistry, 271, 33686-33692.
-
(1996)
Journal of Biological Chemistry
, vol.271
, pp. 33686-33692
-
-
Muriaux, D.1
De., R.H.2
Roques, B.P.3
Paoletti, J.4
-
32
-
-
67049156092
-
Ionic solvation in aqueous and nonaqueous solutions
-
Ohtaki, H. (2001). Ionic solvation in aqueous and nonaqueous solutions. Monatshefte für Chemie, 132, 1237-1268.
-
(2001)
Monatshefte für Chemie
, vol.132
, pp. 1237-1268
-
-
Ohtaki, H.1
-
33
-
-
0142025560
-
Structure and dynamics of hydrated ions
-
Ohtaki, H., & Radnai, T. (1993). Structure and dynamics of hydrated ions. Chemical Reviews, 93, 1157-1204.
-
(1993)
Chemical Reviews
, vol.93
, pp. 1157-1204
-
-
Ohtaki, H.1
Radnai, T.2
-
34
-
-
0029861557
-
A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis
-
Paillart, J.C., Berthoux, L., Ottmann, M., Darlix, J.L., Marquet, R., Ehresmann, B., & Ehresmann, C. (1996). A dual role of the putative RNA dimerization initiation site of human immunodeficiency virus type 1 in genomic RNA packaging and proviral DNA synthesis. Journal of Virology, 70, 8348-8354.
-
(1996)
Journal of Virology
, vol.70
, pp. 8348-8354
-
-
Paillart, J.C.1
Berthoux, L.2
Ottmann, M.3
Darlix, J.L.4
Marquet, R.5
Ehresmann, B.6
Ehresmann, C.7
-
35
-
-
70350741850
-
Molecular dynamics study of the RNA ring nanostructure: A phenomenon of self-stabilization
-
Paliy, M., Melnik, R., & Shapiro, B.A. (2009). Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization. Physical Biology, 6, 046003-046017.
-
(2009)
Physical Biology
, vol.6
, pp. 046003-046017
-
-
Paliy, M.1
Melnik, R.2
Shapiro, B.A.3
-
36
-
-
78349248253
-
Coarse-graining RNA nanostructures for molecular dynamics simulations
-
Paliy, M., Melnik, R., & Shapiro, B.A. (2010). Coarse-graining RNA nanostructures for molecular dynamics simulations. Physical Biology, 7, 036001-036013.
-
(2010)
Physical Biology
, vol.7
, pp. 036001-036013
-
-
Paliy, M.1
Melnik, R.2
Shapiro, B.A.3
-
37
-
-
70349149051
-
New metrics for comparing and assessing discrepancies between RNA 3D structures and models
-
Parisien, M., Cruz, J.A., Westhof, E., & Major, F. (2009). New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA, 15, 1875-1885.
-
(2009)
RNA
, vol.15
, pp. 1875-1885
-
-
Parisien, M.1
Cruz, J.A.2
Westhof, E.3
Major, F.4
-
38
-
-
36849057065
-
Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics
-
Reblova, K., Fadrna, E., Sarzynska, J., Kulinski, T., Kulhanek, P., Ennifar, E., ...Sponer, J. (2007). Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics. Biophysical Journal, 93, 3932-3949.
-
(2007)
Biophysical Journal
, vol.93
, pp. 3932-3949
-
-
Reblova, K.1
Fadrna, E.2
Sarzynska, J.3
Kulinski, T.4
Kulhanek, P.5
Ennifar, E.6
Sponer, J.7
-
39
-
-
17944388579
-
Molecular dynamics simulations of RNA kissingloop motifs reveal structural dynamics and formation of cation-binding pockets
-
Reblova, K., Spackova, N., Sponer, J.E., Koca, J., & Sponer, J. (2003). Molecular dynamics simulations of RNA kissingloop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research, 31, 6942-6952.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 6942-6952
-
-
Reblova, K.1
Spackova, N.2
Sponer, J.E.3
Koca, J.4
Sponer, J.5
-
40
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of nalkanes
-
Ryckaert, J.P., Ciccotti, G., & Berendsen, H.J.C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of nalkanes. Journal of Computational Physics, 23, 327-341.
-
(1977)
Journal of Computational Physics
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
41
-
-
0028239204
-
Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro
-
Skripkin, E., Paillart, J.C., Marquet, R., Ehresmann, B., & Ehresmann, C. (1994). Identification of the primary site of the human immunodeficiency virus type 1 RNA dimerization in vitro. Proceedings of the National Academy of Sciences, 91, 4945-4949.
-
(1994)
Proceedings of the National Academy of Sciences
, vol.91
, pp. 4945-4949
-
-
Skripkin, E.1
Paillart, J.C.2
Marquet, R.3
Ehresmann, B.4
Ehresmann, C.5
-
42
-
-
4944259254
-
Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes
-
Weixlbaumer, A., Werner, A., Flamm, C., Westhof, E., & Schroeder, R. (2004). Determination of thermodynamic parameters for HIV DIS type loop-loop kissing complexes. Nucleic Acids Research, 32, 5126-5133.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 5126-5133
-
-
Weixlbaumer, A.1
Werner, A.2
Flamm, C.3
Westhof, E.4
Schroeder, R.5
-
43
-
-
34548147103
-
Computational design of an RNA hexagonal nanoring and an RNA nanotube
-
Yingling, Y.G., & Shapiro, B.A. (2007). Computational design of an RNA hexagonal nanoring and an RNA nanotube. Nano Letters, 7, 2328-2334.
-
(2007)
Nano Letters
, vol.7
, pp. 2328-2334
-
-
Yingling, Y.G.1
Shapiro, B.A.2
-
44
-
-
0042622381
-
LGA: A method for finding 3D similarities in protein structures
-
Zelma, A. (2003). LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Research, 31, 3370-3374.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3370-3374
-
-
Zelma, A.1
|