-
1
-
-
0036562687
-
Telomere maintenance as a target for anticancer drug discovery
-
Neidle S, Parkinson G, (2002) Telomere maintenance as a target for anticancer drug discovery. Nature Reviews Drug Discovery 1: 383-393.
-
(2002)
Nature Reviews Drug Discovery
, vol.1
, pp. 383-393
-
-
Neidle, S.1
Parkinson, G.2
-
2
-
-
45749103733
-
Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes
-
Huppert JL, (2008) Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chemical Society Reviews 37: 1375-1384.
-
(2008)
Chemical Society Reviews
, vol.37
, pp. 1375-1384
-
-
Huppert, J.L.1
-
3
-
-
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, Šponer J, (2010) Structural dynamics of thrombin-binding dna aptamer d(ggttggtgtggttgg) quadruplex dna studied by large-scale explicit solvent simulations. Journal of Chemical Theory and Computation 6: 3003-3014.
-
(2010)
Journal of Chemical Theory and Computation
, vol.6
, pp. 3003-3014
-
-
Reshetnikov, R.1
Golovin, A.2
Spiridonova, V.3
Kopylov, A.4
Šponer, J.5
-
4
-
-
65249160660
-
Unfolding thermodynamics of intramolecular g-quadruplexes: Base sequence contributions of the loops
-
Olsen CM, Lee HT, Marky LA, (2009) Unfolding thermodynamics of intramolecular g-quadruplexes: Base sequence contributions of the loops. The Journal of Physical Chemistry B 113: 2587-2595.
-
(2009)
The Journal of Physical Chemistry B
, vol.113
, pp. 2587-2595
-
-
Olsen, C.M.1
Lee, H.T.2
Marky, L.A.3
-
5
-
-
0038728819
-
Stability of intramolecular dna quadruplexes: Comparison with dnaduplexes
-
Fox KR, Risitano A, (2003) Stability of intramolecular dna quadruplexes: Comparison with dnaduplexes. Biochemistry 42: 6507-6513.
-
(2003)
Biochemistry
, vol.42
, pp. 6507-6513
-
-
Fox, K.R.1
Risitano, A.2
-
6
-
-
79960699716
-
Loop residues of thrombin-binding dnaaptamer impact g-quadruplex stability and thrombin binding
-
Nagatoishi S, Isono N, Tsumoto K, Sugimoto N, (2011) Loop residues of thrombin-binding dnaaptamer impact g-quadruplex stability and thrombin binding. Biochimie 93: 1231-1238.
-
(2011)
Biochimie
, vol.93
, pp. 1231-1238
-
-
Nagatoishi, S.1
Isono, N.2
Tsumoto, K.3
Sugimoto, N.4
-
7
-
-
11444253374
-
Loop-length-dependent folding of g-quadruplexes
-
Hazel P, Huppert J, Balasubramanian S, Neidle S, (2004) Loop-length-dependent folding of g-quadruplexes. Journal of the American Chemical Society 126: 16405-16415.
-
(2004)
Journal of the American Chemical Society
, vol.126
, pp. 16405-16415
-
-
Hazel, P.1
Huppert, J.2
Balasubramanian, S.3
Neidle, S.4
-
8
-
-
80052569980
-
Insight into g-dna structural polymorphism and fold-ing from sequence and loop connectivity through free energy analysis
-
Cang X, Šponer J, Cheatham TE III, (2011) Insight into g-dna structural polymorphism and fold-ing from sequence and loop connectivity through free energy analysis. Journal of the AmericanChemical Society 133: 14270-14279.
-
(2011)
Journal of the AmericanChemical Society
, vol.133
, pp. 14270-14279
-
-
Cang, X.1
Šponer, J.2
Cheatham III, T.E.3
-
9
-
-
34250878987
-
Defining the mode,energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric g-quadruplex dna
-
Barbieri CM, Srinivasan AR, Rzuczek SG, Rice JE, LaVoie EJ, et al. (2007) Defining the mode,energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric g-quadruplex dna. Nucleic Acids Research 35: 3272-3286.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 3272-3286
-
-
Barbieri, C.M.1
Srinivasan, A.R.2
Rzuczek, S.G.3
Rice, J.E.4
LaVoie, E.J.5
-
10
-
-
47649122998
-
Targeting human telomeric g-quadruplex dna with oxazole-containing macrocyclic compounds
-
Pilch DS, Barbieri CM, Rzuczek SG, LaVoie EJ, Rice JE, (2008) Targeting human telomeric g-quadruplex dna with oxazole-containing macrocyclic compounds. Biochimie 90: 1233-1249.
-
(2008)
Biochimie
, vol.90
, pp. 1233-1249
-
-
Pilch, D.S.1
Barbieri, C.M.2
Rzuczek, S.G.3
LaVoie, E.J.4
Rice, J.E.5
-
11
-
-
35448946080
-
Molecular dynamics simulations and their application to four-strandeddna
-
Šponer J, Špačková N, (2007) Molecular dynamics simulations and their application to four-strandeddna. Methods 43: 278-290.
-
(2007)
Methods
, vol.43
, pp. 278-290
-
-
Šponer, J.1
Špačková, N.2
-
12
-
-
84865084480
-
Molecular dynamics simulations of g-dna and perspectiveson the simulation of nucleic acid structures
-
Šponer J, Cang X, Cheatham TE, (2012) Molecular dynamics simulations of g-dna and perspectiveson the simulation of nucleic acid structures. Methods 57: 25-39.
-
(2012)
Methods
, vol.57
, pp. 25-39
-
-
Šponer, J.1
Cang, X.2
Cheatham, T.E.3
-
13
-
-
84856446581
-
Intramolecular folding in three tandem guanine repeats of human telomeric dna
-
Koirala D, Mashimo T, Sannohe Y, Yu Z, Mao H, et al. (2012) Intramolecular folding in three tandem guanine repeats of human telomeric dna. Chemical Communications 48: 2006-2008.
-
(2012)
Chemical Communications
, vol.48
, pp. 2006-2008
-
-
Koirala, D.1
Mashimo, T.2
Sannohe, Y.3
Yu, Z.4
Mao, H.5
-
14
-
-
84873917136
-
The g-triplex dna
-
Limongelli V, DeTito S, Cerofolini L, Fragai M, Pagano B, et al. (2013) The g-triplex dna. Ange-wandte Chemie International Edition 52: 2269-2273.
-
(2013)
Ange-Wandte Chemie International Edition
, vol.52
, pp. 2269-2273
-
-
Limongelli, V.1
DeTito, S.2
Cerofolini, L.3
Fragai, M.4
Pagano, B.5
-
15
-
-
78649236626
-
Folding pathways of human telomeric type-1 and type-2 g-quadruplex structures
-
Mashimo T, Yagi H, Sannohe Y, Rajendran A, Sugiyama H, (2010) Folding pathways of human telomeric type-1 and type-2 g-quadruplex structures. Journal of the American Chemical Society 132: 14910-14918.
-
(2010)
Journal of the American Chemical Society
, vol.132
, pp. 14910-14918
-
-
Mashimo, T.1
Yagi, H.2
Sannohe, Y.3
Rajendran, A.4
Sugiyama, H.5
-
16
-
-
79961199372
-
Explaining the varied glycosidic conformational, g-tract length and sequence preferences for anti-parallel g-quadruplexes
-
Cang X, Poner J, Cheatham TE, (2011) Explaining the varied glycosidic conformational, g-tract length and sequence preferences for anti-parallel g-quadruplexes. Nucleic Acids Research 39: 4499-4512.
-
(2011)
Nucleic Acids Research
, vol.39
, pp. 4499-4512
-
-
Cang, X.1
Poner, J.2
Cheatham, T.E.3
-
17
-
-
33646359481
-
Predictive modelling of topology and loop variations in dimeric dna quadruplex structures
-
Neidle S, Hazel P, Parkinson GN, (2006) Predictive modelling of topology and loop variations in dimeric dna quadruplex structures. Nucleic Acids Research 34: 2117-2127.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 2117-2127
-
-
Neidle, S.1
Hazel, P.2
Parkinson, G.N.3
-
18
-
-
3042734385
-
Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations
-
Fadrna E, Špačková N, Stefl R, Koca J, Cheatham TE, et al. (2004) Molecular dynamics simulations of guanine quadruplex loops: Advances and force field limitations. Biophysical Journal 87: 227-242.
-
(2004)
Biophysical Journal
, vol.87
, pp. 227-242
-
-
Fadrna, E.1
Špačková, N.2
Stefl, R.3
Koca, J.4
Cheatham, T.E.5
-
19
-
-
0001398008
-
How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules?
-
Wang J, Cieplak P, Kollman PA, (2000) How well does a restrained electrostatic potential (resp) model perform in calculating conformational energies of organic and biological molecules? Journal of Computational Chemistry 21: 1049-1074.
-
(2000)
Journal of Computational Chemistry
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
20
-
-
34250318638
-
Refinenement of the amber force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Orozco M, Perez A, Marchan I, Svozil D, Šponer J, et al. (2007) Refinenement of the amber force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophysical Journal 92: 3817-3829.
-
(2007)
Biophysical Journal
, vol.92
, pp. 3817-3829
-
-
Orozco, M.1
Perez, A.2
Marchan, I.3
Svozil, D.4
Šponer, J.5
-
22
-
-
73349099062
-
Single stranded loops of quadruplex dna as key benchmark for testing nucleic acids force fields
-
Fadrna E, Špačková N, Sarzynska J, Koca J, Orozco M, et al. (2009) Single stranded loops of quadruplex dna as key benchmark for testing nucleic acids force fields. Journal of Chemical Theory and Computation 5: 2514-2530.
-
(2009)
Journal of Chemical Theory and Computation
, vol.5
, pp. 2514-2530
-
-
Fadrna, E.1
Špačková, N.2
Sarzynska, J.3
Koca, J.4
Orozco, M.5
-
23
-
-
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, et al. (2013) Conformational dynamics of the human propeller telomeric dna quadruplex on a microsecond time scale. Nucleic Acids Research 41: 2723-2735.
-
(2013)
Nucleic Acids Research
, vol.41
, pp. 2723-2735
-
-
Islam, B.1
Sgobba, M.2
Laughton, C.3
Orozco, M.4
Sponer, J.5
-
24
-
-
0027918585
-
Solution structure of the human telomeric repeat d[ag(3)(t(2)ag(3))3] g-tetraplex
-
Wang Y, Patel DJ, (1993) Solution structure of the human telomeric repeat d[ag(3)(t(2)ag(3))3] g-tetraplex. Structure 1: 263-282.
-
(1993)
Structure
, vol.1
, pp. 263-282
-
-
Wang, Y.1
Patel, D.J.2
-
25
-
-
0037142071
-
Crystalstructure of parallel quadruplexes from human telomeric dna
-
Neidle S, Parkinson GN, Lee MPH, (2002) Crystalstructure of parallel quadruplexes from human telomeric dna. Nature 417: 876-880.
-
(2002)
Nature
, vol.417
, pp. 876-880
-
-
Neidle, S.1
Parkinson, G.N.2
Lee, M.P.H.3
-
26
-
-
33746600695
-
Structure of the human telomere in k+ solution: An intramolecular (3+1) g-quadruplex scaffold
-
Phan AT, Luu KN, Kuryavyi V, Lacroix L, Patel DJ, (2006) Structure of the human telomere in k+ solution: An intramolecular (3+1) g-quadruplex scaffold. Journal of the American Chemical Society 128: 9963-9970.
-
(2006)
Journal of the American Chemical Society
, vol.128
, pp. 9963-9970
-
-
Phan, A.T.1
Luu, K.N.2
Kuryavyi, V.3
Lacroix, L.4
Patel, D.J.5
-
27
-
-
23844438712
-
Not so crystal clear: the structure of the human telomere g-quadruplex in solution differs from that present in a crystal
-
Li J, Correia JJ, Wang L, Trent JO, Chaires JB, (2005) Not so crystal clear: the structure of the human telomere g-quadruplex in solution differs from that present in a crystal. Nucleic Acids Research 33: 4649-4659.
-
(2005)
Nucleic Acids Research
, vol.33
, pp. 4649-4659
-
-
Li, J.1
Correia, J.J.2
Wang, L.3
Trent, J.O.4
Chaires, J.B.5
-
28
-
-
84555187082
-
Structure and stability of higher-order human telomeric quadruplexes
-
Petraccone L, Spink C, Trent JO, Garbett NC, Mekmaysy CS, et al. (2011) Structure and stability of higher-order human telomeric quadruplexes. Journal of the American Chemical Society 133: 20951-20961.
-
(2011)
Journal of the American Chemical Society
, vol.133
, pp. 20951-20961
-
-
Petraccone, L.1
Spink, C.2
Trent, J.O.3
Garbett, N.C.4
Mekmaysy, C.S.5
-
29
-
-
84863658763
-
Reference simulations of noncanonical nucleic acids with different χ variants of the amber force field: Quadruplex dna, quadruplex rna, and z-dna
-
Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, et al. (2012) Reference simulations of noncanonical nucleic acids with different χ variants of the amber force field: Quadruplex dna, quadruplex rna, and z-dna. Journal of Chemical Theory and Computation 8: 2506-2520.
-
(2012)
Journal of Chemical Theory and Computation
, vol.8
, pp. 2506-2520
-
-
Krepl, M.1
Zgarbová, M.2
Stadlbauer, P.3
Otyepka, M.4
Banáš, P.5
-
30
-
-
0034227603
-
A remarkable alteration in the bonding pattern: An hf and dft study of the interactions between the metal cations and the hoogsteen hydrogen-bonded g-tetrad
-
Leszczynski J, Gu JD, (2000) A remarkable alteration in the bonding pattern: An hf and dft study of the interactions between the metal cations and the hoogsteen hydrogen-bonded g-tetrad. The Journal of Physical Chemistry A 104: 6308-6313.
-
(2000)
The Journal of Physical Chemistry A
, vol.104
, pp. 6308-6313
-
-
Leszczynski, J.1
Gu, J.D.2
-
31
-
-
0345893810
-
Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes
-
Meyer M, Steinke T, Brandl M, Suhnel J, (2001) Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes. Journal of Computational Chemistry 22: 109-124.
-
(2001)
Journal of Computational Chemistry
, vol.22
, pp. 109-124
-
-
Meyer, M.1
Steinke, T.2
Brandl, M.3
Suhnel, J.4
-
32
-
-
0029633186
-
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, et al. (1995) Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications 91: 1-41.
-
(1995)
Computer Physics Communications
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
-
34
-
-
46249092554
-
Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 4: 435-447.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
35
-
-
33750587438
-
Molecular-dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, Vangunsteren WF, Dinola A, Haak JR, (1984) Molecular-dynamics with coupling to an external bath. Journal of Computational Physics 81: 3684-3690.
-
(1984)
Journal of Computational Physics
, 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
-
36
-
-
33846823909
-
Particle mesh ewald - an n.log(n) method for ewald sums in large systems
-
Darden T, York D, Pedersen L, (1993) Particle mesh ewald- an n.log(n) method for ewald sums in large systems. Journal of Computational Physics 98: 10089-10092.
-
(1993)
Journal of Computational Physics
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
37
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML, (1983) Comparison of simple potential functions for simulating liquid water. Journal of Computational Physics 79: 926-935.
-
(1983)
Journal of Computational Physics
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
38
-
-
33646940952
-
Numerical-integration of cartesian equations of motion of a system with constraints - molecular-dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC, (1977) Numerical-integration of cartesian equations of motion of a system with constraints- molecular-dynamics of n-alkanes. 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
-
39
-
-
0032560959
-
Continuumsolvent studies of the stability of dna, rna, and phosphoramidatedna helices
-
Srinivasan J, Cheatham TE, Cieplak P, Kollman PA, Case DA, (1998) Continuumsolvent studies of the stability of dna, rna, and phosphoramidatedna helices. Journal of the American Chemical Society 120: 9401-9409.
-
(1998)
Journal of the American Chemical Society
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
40
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA, (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America 98: 10037-10041.
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
41
-
-
0029126044
-
The assessment of the geometry of dinucleotide steps in double-helical dna - a new local calculation scheme
-
El hassan MA, Calladine CR, (1995) The assessment of the geometry of dinucleotide steps in double-helical dna- a new local calculation scheme. Journal of Molecular Biology 251: 648-664.
-
(1995)
Journal of Molecular Biology
, vol.251
, pp. 648-664
-
-
El hassan, M.A.1
Calladine, C.R.2
-
42
-
-
0031592942
-
Structure and conformation of helical nucleic acids: Analysis program (schnaap)
-
Lu XJ, ElHassan MA, Hunter CA, (1997) Structure and conformation of helical nucleic acids: Analysis program (schnaap). Journal of Molecular Biology 273: 668-680.
-
(1997)
Journal of Molecular Biology
, vol.273
, pp. 668-680
-
-
Lu, X.J.1
ElHassan, M.A.2
Hunter, C.A.3
-
43
-
-
79958185452
-
Software news and updates md-analysis: A toolkit for the analysis of molecular dynamics simulations
-
Woolf TB, Michaud-Agrawal N, Denning EJ, Beckstein O, (2011) Software news and updates md-analysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry 32: 2319-2327.
-
(2011)
Journal of Computational Chemistry
, vol.32
, pp. 2319-2327
-
-
Woolf, T.B.1
Michaud-Agrawal, N.2
Denning, E.J.3
Beckstein, O.4
-
44
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
Olson WK, Bansal M, Burley SK, Dickerson RE, Gerstein M, et al. (2001) A standard reference frame for the description of nucleic acid base-pair geometry. Journal of Molecular Biology 313: 229-237.
-
(2001)
Journal of Molecular Biology
, vol.313
, pp. 229-237
-
-
Olson, W.K.1
Bansal, M.2
Burley, S.K.3
Dickerson, R.E.4
Gerstein, M.5
-
45
-
-
0242396923
-
3dna: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Olson WK, Lu XJ, (2003) 3dna: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Research 31: 5108-5121.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 5108-5121
-
-
Olson, W.K.1
Lu, X.J.2
|