-
1
-
-
33751020853
-
Quadruplex DNA: Sequence, topology and structure
-
Burge S., Parkinson G.N., Hazel P., Todd A.K. and Neidle S. (2006) Quadruplex DNA: Sequence, topology and structure. Nucleic Acids Res., 34, 5402-5415
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5402-5415
-
-
Burge, S.1
Parkinson, G.N.2
Hazel, P.3
Todd, A.K.4
Neidle, S.5
-
2
-
-
37049004147
-
Targeting telomeres and telomerase
-
De Cian A., Lacroix L., Douarre C., Temime-Smaali N., Trentesaux C., Riou J.F. and Mergny J.L. (2008) Targeting telomeres and telomerase. Biochimie, 90, 131-155
-
(2008)
Biochimie
, vol.90
, pp. 131-155
-
-
De Cian, A.1
Lacroix, L.2
Douarre, C.3
Temime-Smaali, N.4
Trentesaux, C.5
Riou, J.F.6
Mergny, J.L.7
-
3
-
-
47849105417
-
Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions
-
Qin Y. and Hurley L.H. (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie, 90, 1149-1171
-
(2008)
Biochimie
, vol.90
, pp. 1149-1171
-
-
Qin, Y.1
Hurley, L.H.2
-
4
-
-
45749103733
-
Four-stranded nucleic acids: Structure function and targeting of G-quadruplexes
-
Huppert J.L. (2008) Four-stranded nucleic acids: Structure, function and targeting of G-quadruplexes. Chem. Soc. Rev., 37, 1375-1384
-
(2008)
Chem. Soc. Rev
, vol.37
, pp. 1375-1384
-
-
Huppert, J.L.1
-
5
-
-
66549124907
-
The structures of quadruplex nucleic acids and their drug complexes
-
Neidle S. (2009) The structures of quadruplex nucleic acids and their drug complexes. Curr. Opin. Struct. Biol., 19, 239-250
-
(2009)
Curr. Opin. Struct. Biol
, vol.19
, pp. 239-250
-
-
Neidle, S.1
-
6
-
-
77955834769
-
Structure, location and interactions of G-quadruplexes
-
Huppert J.L. (2010) Structure, location and interactions of G-quadruplexes. FEBS J., 277, 3452-3458
-
(2010)
FEBS J.
, vol.277
, pp. 3452-3458
-
-
Huppert, J.L.1
-
7
-
-
76349122184
-
Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer
-
Neidle S. (2010) Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J., 277, 1118-1125
-
(2010)
FEBS J.
, vol.277
, pp. 1118-1125
-
-
Neidle, S.1
-
8
-
-
79959509289
-
Structure of human telomeric DNA in crowded solution
-
Heddi B. and Phan A.T. (2011) Structure of human telomeric DNA in crowded solution. J. Am. Chem. Soc., 133, 9824-9833
-
(2011)
J. Am. Chem. Soc
, vol.133
, pp. 9824-9833
-
-
Heddi, B.1
Phan, A.T.2
-
9
-
-
37249066753
-
Geometric formalism for DNA quadruplex folding
-
Silva M.W. (2007) Geometric formalism for DNA quadruplex folding. Chem. Eur. J., 13, 9738-9745
-
(2007)
Chem. Eur. J.
, vol.13
, pp. 9738-9745
-
-
Silva, M.W.1
-
10
-
-
0038202304
-
Small change in a G-rich sequence a dramatic change in topology: New dimeric G-quadruplex folding motif with unique loop orientations
-
Crnugelj M., Sket P. and Plavec J. (2003) Small change in a G-rich sequence, a dramatic change in topology: New dimeric G-quadruplex folding motif with unique loop orientations. J. Am. Chem. Soc., 125, 7866-7871
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 7866-7871
-
-
Crnugelj, M.1
Sket, P.2
Plavec, J.3
-
11
-
-
3242666778
-
Propeller-Type parallel-stranded G-quadruplexes in the human c-myc promoter
-
Phan A.T., Modi Y.S. and Patel D.J. (2004) Propeller-Type parallel-stranded G-quadruplexes in the human c-myc promoter. J. Am. Chem. Soc., 126, 8710-8716
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 8710-8716
-
-
Phan, A.T.1
Modi, Y.S.2
Patel, D.J.3
-
12
-
-
33746600695
-
Structure of the human telomere in K+solution: An intramolecular (3+1) G-quadruplex scaffold
-
Luu K.N., Phan A.T., Kuryavyi V., Lacroix L. and Patel D.J. (2006) Structure of the human telomere in K+solution: An intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 9963-9970
-
-
Luu, K.N.1
Phan, A.T.2
Kuryavyi, V.3
Lacroix, L.4
Patel, D.J.5
-
14
-
-
47249089630
-
Polymorphism of human telomeric quadruplex structures
-
Dai J.X., Carver M. and Yang D.Z. (2008) Polymorphism of human telomeric quadruplex structures. Biochimie, 90, 1172-1183
-
(2008)
Biochimie
, vol.90
, pp. 1172-1183
-
-
Dai, J.X.1
Carver, M.2
Yang, D.Z.3
-
15
-
-
33646943863
-
Human telomeric sequence forms a hybrid-Type intramolecular G-quadruplex structure with mixed parallel/ antiparallel strands in potassium solution
-
Ambrus A., Chen D., Dai J.X., Bialis T., Jones R.A. and Yang D.Z. (2006) Human telomeric sequence forms a hybrid-Type intramolecular G-quadruplex structure with mixed parallel/ antiparallel strands in potassium solution. Nucleic Acids Res., 34, 2723-2735
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 2723-2735
-
-
Ambrus, A.1
Chen, D.2
Dai, J.X.3
Bialis, T.4
Jones, R.A.5
Yang, D.Z.6
-
16
-
-
78649236626
-
Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures
-
Mashimo T., Yagi H., Sannohe Y., Rajendran A. and Sugiyama H. (2010) Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures. J. Am. Chem. Soc., 132, 14910-14918
-
(2010)
J. Am. Chem. Soc
, vol.132
, pp. 14910-14918
-
-
Mashimo, T.1
Yagi, H.2
Sannohe, Y.3
Rajendran, A.4
Sugiyama, H.5
-
17
-
-
84862227693
-
Energetic basis of human telomeric DNA folding into G-quadruplex structures
-
Boncina M., Lah J., Prislan I. and Vesnaver G. (2012) Energetic basis of human telomeric DNA folding into G-quadruplex structures. J. Am. Chem. Soc., 134, 9657-9663
-
(2012)
J. Am. Chem. Soc
, vol.134
, pp. 9657-9663
-
-
Boncina, M.1
Lah, J.2
Prislan, I.3
Vesnaver, G.4
-
18
-
-
84856446581
-
Intramolecular folding in three tandem guanine repeats of human telomeric DNA
-
Koirala D., Mashimo T., Sannohe Y., Yu Z.B., Mao H.B. and Sugiyama H. (2012) Intramolecular folding in three tandem guanine repeats of human telomeric DNA. Chem. Commun., 48, 2006-2008
-
(2012)
Chem. Commun
, vol.48
, pp. 2006-2008
-
-
Koirala, D.1
Mashimo, T.2
Sannohe, Y.3
Yu, Z.B.4
Mao, H.B.5
Sugiyama, H.6
-
19
-
-
84865075446
-
Isothermal folding of G-quadruplexes
-
Gray R.D. and Chaires J.B. (2012) Isothermal folding of G-quadruplexes. Methods, 57, 47-55
-
(2012)
Methods
, vol.57
, pp. 47-55
-
-
Gray, R.D.1
Chaires, J.B.2
-
20
-
-
0032508468
-
Following G-quartet formation by UV-spectroscopy
-
Mergny J.L., Phan A.T. and Lacroix L. (1998) Following G-quartet formation by UV-spectroscopy. FEBS Lett., 435, 74-78
-
(1998)
FEBS Lett
, vol.435
, pp. 74-78
-
-
Mergny, J.L.1
Phan, A.T.2
Lacroix, L.3
-
21
-
-
77956098867
-
Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry
-
Rosu F., Gabelica V., Poncelet H. and De Pauw E. (2010) Tetramolecular G-quadruplex formation pathways studied by electrospray mass spectrometry. Nucleic Acids Res., 38, 5217-5225
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 5217-5225
-
-
Rosu, F.1
Gabelica, V.2
Poncelet, H.3
De Pauw, E.4
-
22
-
-
39349084354
-
The formation pathway of tetramolecular G-quadruplexes
-
Bardin C. and Leroy J.L. (2008) The formation pathway of tetramolecular G-quadruplexes. Nucleic Acids Res., 36, 477-488
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 477-488
-
-
Bardin, C.1
Leroy, J.L.2
-
23
-
-
84867366926
-
Populated intermediates in the thermal unfolding of the human telomeric quadruplex
-
Gray R.D., Buscaglia R. and Chaires J.B. (2012) Populated intermediates in the thermal unfolding of the human telomeric quadruplex. J. Am. Chem. Soc., 134, 16834-16844
-
(2012)
J. Am. Chem. Soc
, vol.134
, pp. 16834-16844
-
-
Gray, R.D.1
Buscaglia, R.2
Chaires, J.B.3
-
24
-
-
65249175153
-
Energetics and kinetics of a conformational switch in G-Quadruplex DNA
-
Gray R.D., Li J. and Chaires J.B. (2009) Energetics and kinetics of a conformational switch in G-Quadruplex DNA. J. Phys. Chem. B, 113, 2676-2683
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2676-2683
-
-
Gray, R.D.1
Li, J.2
Chaires, J.B.3
-
25
-
-
0344304471
-
Studies on the structure and dynamics of the human telomeric G-quadruplex by single-molecule fluorescence resonance energy transfer
-
Ying L.M., Green J.J., Li H.T., Klenerman D. and Balasubramanian S. (2003) Studies on the structure and dynamics of the human telomeric G-quadruplex by single-molecule fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA, 100, 14629-14634
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 14629-14634
-
-
Ying, L.M.1
Green, J.J.2
Li, H.T.3
Klenerman, D.4
Balasubramanian, S.5
-
26
-
-
33746611174
-
Investigating a quadruplex-ligand interaction by unfolding kinetics
-
Green J.J., Ladame S., Ying L.M., Klenerman D. and Balasubramanian S. (2006) Investigating a quadruplex-ligand interaction by unfolding kinetics. J. Am. Chem. Soc., 128, 9809-9812
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 9809-9812
-
-
Green, J.J.1
Ladame, S.2
Ying, L.M.3
Klenerman, D.4
Balasubramanian, S.5
-
27
-
-
77950344651
-
Structure of a two-G-Tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+solution: Insights into the interconversion of human telomeric G-quadruplex structures
-
Zhang Z.J., Dai J.X., Veliath E., Jones R.A. and Yang D.Z. (2010) Structure of a two-G-Tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+solution: Insights into the interconversion of human telomeric G-quadruplex structures. Nucleic Acids Res., 38, 1009-1021
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1009-1021
-
-
Zhang, Z.J.1
Dai, J.X.2
Veliath, E.3
Jones, R.A.4
Yang, D.Z.5
-
28
-
-
30044448463
-
Extreme conformational diversity in human telomeric DNA
-
Lee J.Y., Okumus B., Kim D.S. and Ha T.J. (2005) Extreme conformational diversity in human telomeric DNA. Proc. Natl Acad. Sci. USA, 102, 18938-18943
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 18938-18943
-
-
Lee, J.Y.1
Okumus, B.2
Kim, D.S.3
Ha, T.J.4
-
29
-
-
0001505226
-
Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids
-
Hardin C.C., Perry A.G. and White K. (2001) Thermodynamic and kinetic characterization of the dissociation and assembly of quadruplex nucleic acids. Biopolymers, 56, 147-194
-
(2001)
Biopolymers
, vol.56
, pp. 147-194
-
-
Hardin, C.C.1
Perry, A.G.2
White, K.3
-
30
-
-
33646345847
-
Unfolding of G-quadruplexes: Energetic, and ion and water contributions of G-quartet stacking
-
Olsen C.M., Gmeiner W.H. and Marky L.A. (2006) Unfolding of G-quadruplexes: Energetic, and ion and water contributions of G-quartet stacking. J. Phys. Chem. B, 110, 6962-6969
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 6962-6969
-
-
Olsen, C.M.1
Gmeiner, W.H.2
Marky, L.A.3
-
31
-
-
84869478580
-
The kinetics and folding pathways of intramolecular g-quadruplex nucleic acids
-
Zhang A.Y.Q. and Balasubramanian S. (2012) The Kinetics and Folding Pathways of Intramolecular G-Quadruplex Nucleic Acids. J. Am. Chem. Soc., 134, 19297-19308
-
(2012)
J. Am. Chem. Soc
, vol.134
, pp. 19297-19308
-
-
Zhang, A.Y.Q.1
Balasubramanian, S.2
-
32
-
-
47249114945
-
Kinetics and mechanism of K(+)-And Na(+)-induced folding of models of human telomeric DNA into G-quadruplex structures
-
Gray R.D. and Chaires J.B. (2008) Kinetics and mechanism of K(+)-And Na(+)-induced folding of models of human telomeric DNA into G-quadruplex structures. Nucleic Acids Res., 36, 4191-4203
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 4191-4203
-
-
Gray, R.D.1
Chaires, J.B.2
-
33
-
-
83755185482
-
Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process
-
Reshetnikov R.V., Sponer J., Rassokhina O.I., Kopylov A.M., Tsvetkov P.O., Makarov A.A. and Golovin A.V. (2011) Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process. Nucleic Acids Res., 39, 9789-9802
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 9789-9802
-
-
Reshetnikov, R.V.1
Sponer, J.2
Rassokhina, O.I.3
Kopylov, A.M.4
Tsvetkov, P.O.5
Makarov, A.A.6
Golovin, A.V.7
-
34
-
-
78249249624
-
Multiple routes to characterize the folding of a small DNA hairpin
-
Portella G. and Orozco M. (2010) Multiple routes to characterize the folding of a small DNA hairpin. Angew. Chem., Int. Ed. Engl., 49, 7673-7676
-
(2010)
Angew. Chem., Int. Ed. Engl
, vol.49
, pp. 7673-7676
-
-
Portella, G.1
Orozco, M.2
-
35
-
-
35448946080
-
Molecular dynamics simulations and their application to four-stranded DNA
-
Sponer J. and Spackova N. (2007) Molecular dynamics simulations and their application to four-stranded DNA. Methods, 43, 278-290
-
(2007)
Methods
, vol.43
, pp. 278-290
-
-
Sponer, J.1
Spackova, N.2
-
36
-
-
84865084480
-
Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures
-
Sponer J., Cang X.H. and Cheatham T.E. (2012) Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods, 57, 25-39
-
(2012)
Methods
, vol.57
, pp. 25-39
-
-
Sponer, J.1
Cang, X.H.2
Cheatham, T.E.3
-
37
-
-
77957958900
-
Structural dynamics of thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations
-
Reshetnikov R., Golovin A., Spiridonova V., Kopylov A. and Sponer J. (2010) Structural dynamics of thrombin-binding DNA aptamer d(GGTTGGTGTGGTTGG) quadruplex DNA studied by large-scale explicit solvent simulations. J. Chem. Theory Comput., 6, 3003-3014
-
(2010)
J. Chem. Theory Comput
, vol.6
, pp. 3003-3014
-
-
Reshetnikov, R.1
Golovin, A.2
Spiridonova, V.3
Kopylov, A.4
Sponer, J.5
-
38
-
-
0042823487
-
Formation pathways of a guaninequadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates
-
Stefl R., Cheatham T.E., Spackova N., Fadrna E., Berger I., Koca J. and Sponer J. (2003) Formation pathways of a guaninequadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys. J., 85, 1787-1804
-
(2003)
Biophys. J.
, vol.85
, pp. 1787-1804
-
-
Stefl, R.1
Cheatham, T.E.2
Spackova, N.3
Fadrna, E.4
Berger, I.5
Koca, J.6
Sponer, J.7
-
39
-
-
58149288068
-
Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study
-
Li H., Cao E.H. and Gisler T. (2009) Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study. Biochem. Biophys. Res. Commun., 379, 70-75
-
(2009)
Biochem. Biophys. Res. Commun
, vol.379
, pp. 70-75
-
-
Li, H.1
Cao, E.H.2
Gisler, T.3
-
40
-
-
83755185701
-
Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+
-
Yang C., Jang S. and Pak Y. (2011) Multiple stepwise pattern for potential of mean force in unfolding the thrombin binding aptamer in complex with Sr2+. J. Chem. Phys., 135, 225104
-
(2011)
J. Chem. Phys
, vol.135
, pp. 225104
-
-
Yang, C.1
Jang, S.2
Pak, Y.3
-
41
-
-
84869008079
-
Free-energy landscape of a thrombin-binding DNA aptamer in aqueous environment
-
Kim E., Yang C. and Pak Y. (2012) Free-energy landscape of a thrombin-binding DNA aptamer in aqueous environment. J. Chem. Theory Comput., 8, 4845-4851
-
(2012)
J. Chem. Theory Comput
, vol.8
, pp. 4845-4851
-
-
Kim, E.1
Yang, C.2
Pak, Y.3
-
42
-
-
84873917136
-
The g-Triplex dna
-
Limongelli V., De Tito S., Cerofolini L., Fragai M., Pagano B., Trotta R., Cosconati S., Marinelli L., Novellino E., Bertini I. et al. (2013) The G-Triplex DNA. Angew. Chem. Int. Ed. Engl., 52, 2269-2273
-
(2013)
Angew. Chem. Int. Ed. Engl
, vol.52
, pp. 2269-2273
-
-
Limongelli, V.1
De Tito, S.2
Cerofolini, L.3
Fragai, M.4
Pagano, B.5
Trotta, R.6
Cosconati, S.7
Marinelli, L.8
Novellino, E.9
Bertini, I.10
-
43
-
-
33847201903
-
Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations
-
Beck D.A.C., White G.W.N. and Daggett V. (2007) Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations. J. Struct. Biol., 157, 514-523
-
(2007)
J. Struct. Biol
, vol.157
, pp. 514-523
-
-
Beck, D.A.C.1
White, G.W.N.2
Daggett, V.3
-
44
-
-
84875989318
-
Computer folding of RNA tetraloops? Are we there yet
-
Kührová,P., Banáš,P., Best R.B., Š poner J. and Otyepka M. (2013) Computer folding of RNA tetraloops? Are we there yet? J. Chem. Theory Comput., 9, 1461-1468
-
(2013)
J. Chem. Theory Comput
, vol.9
, pp. 1461-1468
-
-
Kührová, P.1
Banáš, P.2
Best, R.B.3
Šponer, J.4
Otyepka, M.5
-
45
-
-
0037142071
-
Crystal structure of parallel quadruplexes from human telomeric DNA
-
Parkinson G.N., Lee M.P.H. and Neidle S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880
-
(2002)
Nature
, vol.417
, pp. 876-880
-
-
Parkinson, G.N.1
Lee, M.P.H.2
Neidle, S.3
-
46
-
-
0036290781
-
Crystal structure of the potassium form of an Oxytricha nova G-quadruplex
-
Haider S., Parkinson G.N. and Neidle S. (2002) Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J. Mol. Biol., 320, 189-200
-
(2002)
J. Mol. Biol
, vol.320
, pp. 189-200
-
-
Haider, S.1
Parkinson, G.N.2
Neidle, S.3
-
47
-
-
0031576353
-
The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution
-
Phillips K., Dauter Z., Murchie A.I.H., Lilley D.M.J. and Luisi B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution. J. Mol. Biol., 273, 171-182
-
(1997)
J. Mol. Biol
, vol.273
, pp. 171-182
-
-
Phillips, K.1
Dauter, Z.2
Murchie, A.I.H.3
Lilley, D.M.J.4
Luisi, B.5
-
48
-
-
0035923718
-
X-ray analysis of an RNA tetraplex (UGGGGU (4) with divalent Sr2+ions at subatomic resolution (0.61 angstrom)
-
Deng J.P., Xiong Y. and Sundaralingam M. (2001) X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr2+ions at subatomic resolution (0.61 angstrom). Proc. Natl Acad. Sci. USA, 98, 13665-13670
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 13665-13670
-
-
Deng, J.P.1
Xiong, Y.2
Sundaralingam, M.3
-
49
-
-
84863191355
-
The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages
-
Clark G.R., Pytel P.D. and Squire C.J. (2012) The high-resolution crystal structure of a parallel intermolecular DNA G-4 quadruplex/drug complex employing syn glycosyl linkages. Nucleic Acids Res., 40, 5731-5738
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5731-5738
-
-
Clark, G.R.1
Pytel, P.D.2
Squire, C.J.3
-
50
-
-
30344440627
-
-
University of California, San Francisco, CA
-
Case D.A., Darden T.A., Cheatham T.E. III, Simmerling C.L., Wang J., Duke R.E., Luo R., Crowley M., Walker R.C., Zhang W. et al. (2008) AMBER 10. University of California, San Francisco, CA.
-
(2008)
AMBER
, vol.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
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
-
51
-
-
0004016501
-
Comparison of simle potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W. and Klein M.L. (1983) Comparison of simle potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935
-
(1983)
J. Chem. Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
52
-
-
0344796204
-
Ion water interaction potentials derived from free-energy perturbation simulations
-
Aqvist J. (1990) Ion water interaction potentials derived from free-energy perturbation simulations. J. Phys. Chem., 94, 8021-8024
-
(1990)
J. Phys. Chem
, vol.94
, pp. 8021-8024
-
-
Aqvist, J.1
-
53
-
-
0011108916
-
Computer simulations of NaCl association in polarizable water
-
Smith D.E. and Dang L.X. (1994) Computer simulations of NaCl association in polarizable water. J. Chem. Phys., 100, 3757-3766
-
(1994)
J. Chem. Phys
, vol.100
, pp. 3757-3766
-
-
Smith, D.E.1
Dang, L.X.2
-
54
-
-
35948966376
-
Spontaneous formation of KCl aggregates in biomolecular simulations: A force field issué
-
Auffinger P., Cheatham T.E. and Vaiana A.C. (2007) Spontaneous formation of KCl aggregates in biomolecular simulations: A force field issué J. Chem. Theory Comput., 3, 1851-1859
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 1851-1859
-
-
Auffinger, P.1
Cheatham, T.E.2
Vaiana, A.C.3
-
55
-
-
49449085241
-
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
-
Joung I.S. and Cheatham T.E. (2008) Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J. Phys. Chem. B, 112, 9020-9041
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
56
-
-
34250318638
-
Refinenement 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., Laughton C.A. and Orozco M. (2007) Refinenement 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
-
-
Perez, A.1
Marchan, I.2
Svozil, D.3
Sponer, J.4
Cheatham, T.E.5
Laughton, C.A.6
Orozco, M.7
-
57
-
-
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., 117, 5179-5197
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
58
-
-
84863658763
-
Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA
-
Krepl M., Zgarbova M., Stadlbauer P., Otyepka M., Banas P., Koca J., Cheatham T.E., Jurecka P. and Sponer J. (2012) Reference simulations of noncanonical nucleic acids with different chi variants of the AMBER force field: Quadruplex DNA, quadruplex RNA, and Z-DNA. J. Chem. Theory Comput., 8, 2506-2520
-
(2012)
J. Chem. Theory Comput
, vol.8
, pp. 2506-2520
-
-
Krepl, M.1
Zgarbova, M.2
Stadlbauer, P.3
Otyepka, M.4
Banas, P.5
Koca, J.6
Cheatham, T.E.7
Jurecka, P.8
Sponer, J.9
-
59
-
-
78651294111
-
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
-
Banas P., Hollas D., Zgarbova M., Jurecka P., Orozco M., Cheatham T.E., Sponer J. and Otyepka M. (2010) Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins. J. Chem. Theory Comput., 6, 3836-3849
-
(2010)
J. Chem. Theory Comput
, vol.6
, pp. 3836-3849
-
-
Banas, P.1
Hollas, D.2
Zgarbova, M.3
Jurecka, P.4
Orozco, M.5
Cheatham, T.E.6
Sponer, J.7
Otyepka, M.8
-
60
-
-
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. 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, T.E.6
Jurecka, P.7
-
61
-
-
84870918415
-
-
University of California, San Francisco, CA
-
Case D.A., Darden T.A., Cheatham T.E III, Simmerling C.L., Wang J., Duke R.E., Luo R., Walker R.C., Zhang W., Merz K.M.R. et al. (2012) AMBER 12. University of California, San Francisco, CA.
-
(2012)
AMBER
, vol.12
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.R.10
-
62
-
-
84860767348
-
Routine microsecond molecular dynamics simulations with amber on gpus 1
-
Gotz A.W., Williamson M.J., Xu D., Poole D., Le Grand S. and Walker R.C. (2012) Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized Born. J. Chem. Theory Comput., 8, 1542-1555
-
(2012)
Generalized Born. J. Chem. Theory Comput
, vol.8
, pp. 1542-1555
-
-
Gotz, A.W.1
Williamson, M.J.2
Xu, D.3
Poole, D.4
Le Grand, S.5
Walker, R.C.6
-
63
-
-
84868214675
-
Spfp: Speed without compromise a mixed precision model for gpu accelerated molecular dynamics simulations
-
Le Grand S., Götz A.W. and Walker R.C. (2013) SPFP: Speed without compromise-A mixed precision model for GPU accelerated molecular dynamics simulations. Comput. Phys. Commun., 184, 374-380
-
(2013)
Comput. Phys. Commun
, vol.184
, pp. 374-380
-
-
Le Grand, S.1
Götz, A.W.2
Walker, R.C.3
-
64
-
-
33846823909
-
Particle mesh ewald-An nlog(n) method for ewald sums in large systems
-
Darden T., York D. and Pedersen L. (1993) Particle mesh Ewald-An N.log(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092
-
(1993)
J. Chem. Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
65
-
-
33645961739
-
A smooth particle mesh ewald method
-
Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H. and Pedersen L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8593
-
(1995)
J. Chem. Phys
, 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
-
66
-
-
33646940952
-
Numerical integration of cartesian equations of motion of a system with constraints-molecular dynamics of n-Alkans
-
Ryckaert J.P., Ciccotti G. and Berendsen H.J.C. (1977) Numerical integration of cartesian equations of motion of a system with constraints-Molecular dynamics of N-Alkans. J. Comput. Phys., 23, 327-341
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
67
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
Berendsen H.J.C., Postma J.P.M., Vangunsteren W.F., Dinola A. and Haak J.R. (1984) Molecular-dynamics with coupling to an external bath. J. Chem. Phys., 81, 3684-3690
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
69
-
-
0035576327
-
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
-
GelpíJ.L., Kalko S.G., Barril X., Cirera J., de La Cruz X., Luque F.J. and Orozco M. (2001) Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins. Proteins, 45, 428-437
-
(2001)
Proteins
, vol.45
, pp. 428-437
-
-
Gelpí, J.L.1
Kalko, S.G.2
Barril, X.3
Cirera, J.4
De La Cruz, X.5
Luque, F.J.6
Orozco, M.7
-
70
-
-
0034836422
-
Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations
-
Spackova N., Berger I. and Sponer J. (2001) Structural dynamics and cation interactions of DNA quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale MD simulations. J. Am. Chem. Soc., 123, 3295-3307
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 3295-3307
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
71
-
-
33846338144
-
Stability and migration of metal ions in G4-wires by molecular dynamics simulations
-
Cavallari M., Calzolari A., Garbesi A. and Di Felice R. (2006) Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J. Phys. Chem. B, 110, 26337-26348
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 26337-26348
-
-
Cavallari, M.1
Calzolari, A.2
Garbesi, A.3
Di Felice, R.4
-
72
-
-
84876390933
-
Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale
-
Islam B., Sgobba M., Laughton C., Orozco M., Sponer J., Neidle S. and Haider S. (2013) Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Res., 41, 2723-2735
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 2723-2735
-
-
Islam, B.1
Sgobba, M.2
Laughton, C.3
Orozco, M.4
Sponer, J.5
Neidle, S.6
Haider, S.7
-
73
-
-
0040164390
-
Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules
-
Spackova N., Berger I. and Sponer J. (1999) Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. J. Am. Chem. Soc., 121, 5519-5534
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 5519-5534
-
-
Spackova, N.1
Berger, I.2
Sponer, J.3
-
74
-
-
34250346492
-
NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution
-
Podbevsek P., Hud N.V. and Plavec J. (2007) NMR evaluation of ammonium ion movement within a unimolecular G-quadruplex in solution. Nucleic Acids Res., 35, 2554-2563
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 2554-2563
-
-
Podbevsek, P.1
Hud, N.V.2
Plavec, J.3
-
75
-
-
3042734385
-
Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
-
Fadrna E., Spackova N., Stefl R., Koca J., Cheatham T.E. and Sponer J. (2004) Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophys. J., 87, 227-242
-
(2004)
Biophys. J.
, vol.87
, pp. 227-242
-
-
Fadrna, E.1
Spackova, N.2
Stefl, R.3
Koca, J.4
Cheatham, T.E.5
Sponer, J.6
-
76
-
-
73349099062
-
Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields
-
Fadrna E., Spackova N., Sarzynska J., Koca J., Orozco M., Cheatham T.E., Kulinski T. and Sponer J. (2009) Single stranded loops of quadruplex DNA as key benchmark for testing nucleic acids force fields. J. Chem. Theory Comput., 5, 2514-2530
-
(2009)
J. Chem. Theory Comput
, vol.5
, pp. 2514-2530
-
-
Fadrna, E.1
Spackova, N.2
Sarzynska, J.3
Koca, J.4
Orozco, M.5
Cheatham, T.E.6
Kulinski, T.7
Sponer, J.8
-
77
-
-
79961199372
-
Explaining the varied glycosidic conformational, G-Tract length and sequence preferences for anti-parallel G-quadruplexes
-
Cang X.H., Sponer J. and Cheatham T.E. (2011) Explaining the varied glycosidic conformational, G-Tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res., 39, 4499-4512
-
(2011)
Nucleic Acids Res
, vol.39
, pp. 4499-4512
-
-
Cang, X.H.1
Sponer, J.2
Cheatham, T.E.3
-
78
-
-
84870581528
-
Strand directionality affects cation binding and movement within tetramolecular G-quadruplexes
-
Š ket P., Virgilio A., Esposito V., Galeone A. and Plavec J. (2012) Strand directionality affects cation binding and movement within tetramolecular G-quadruplexes. Nucleic Acids Res., 40, 11047-11057
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 11047-11057
-
-
Šket, P.1
Virgilio, A.2
Esposito, V.3
Galeone, A.4
Plavec, J.5
-
79
-
-
77956428377
-
Tetramolecular DNA quadruplexes in solution: Insights into structural diversity and cation movement
-
Š ket P. and Plavec J. (2010) Tetramolecular DNA quadruplexes in solution: Insights into structural diversity and cation movement. J. Am. Chem. Soc., 132, 12724-12732
-
(2010)
J. Am. Chem. Soc
, vol.132
, pp. 12724-12732
-
-
Šket, P.1
Plavec, J.2
-
80
-
-
0030015009
-
Kinetics of G-quartet-mediated tetramer formation
-
Wyatt J.R., Davis P.W. and Freier S.M. (1996) Kinetics of G-quartet-mediated tetramer formation. Biochemistry, 35, 8002-8008
-
(1996)
Biochemistry
, vol.35
, pp. 8002-8008
-
-
Wyatt, J.R.1
Davis, P.W.2
Freier, S.M.3
-
81
-
-
13744249293
-
Kinetics of tetramolecular quadruplexes
-
Mergny J.L., De Cian A., Ghelab A., Sacca B. and Lacroix L. (2005) Kinetics of tetramolecular quadruplexes. Nucleic Acids Res., 33, 81-94
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 81-94
-
-
Mergny, J.L.1
De Cian, A.2
Ghelab, A.3
Sacca, B.4
Lacroix, L.5
-
82
-
-
34250682662
-
Guanines are a quartet's best friend: Impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes
-
Gros J., Rosu F., Amrane S., De Cian A., Gabelica V., Lacroix L. and Mergny J.L. (2007) Guanines are a quartet's best friend: Impact of base substitutions on the kinetics and stability of tetramolecular quadruplexes. Nucleic Acids Res., 35, 3064-3075
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3064-3075
-
-
Gros, J.1
Rosu, F.2
Amrane, S.3
De Cian, A.4
Gabelica, V.5
Lacroix, L.6
Mergny, J.L.7
|