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For: Chowdhury S, Bansal M. A nanosecond molecular dynamics study of antiparallel d(G)7 quadruplex structures: effect of the coordinated cations. J Biomol Struct Dyn 2001;18:647-69. [PMID: 11334103 DOI: 10.1080/07391102.2001.10506696] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Number Cited by Other Article(s)
1
Chakraborty K, Khatua P, Bandyopadhyay S. Exploring ion induced folding of a single-stranded DNA oligomer from molecular simulation studies. Phys Chem Chem Phys 2016;18:15899-910. [PMID: 27241311 DOI: 10.1039/c6cp00663a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
2
Ali A, Bansal M, Bhattacharya S. Ligand 5,10,15,20-tetra(N-methyl-4-pyridyl)porphine (TMPyP4) prefers the parallel propeller-type human telomeric G-quadruplex DNA over its other polymorphs. J Phys Chem B 2014;119:5-14. [PMID: 25526532 DOI: 10.1021/jp505792z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
3
šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012;57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022]  Open
4
Fadrná E, Špačková N, Sarzyñska J, Koča J, Orozco M, Cheatham TE, Kulinski T, Šponer J. Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields. J Chem Theory Comput 2009;5:2514-30. [DOI: 10.1021/ct900200k] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
5
Targeting DNA quadruplexes with distamycin A and its derivatives: An ITC and NMR study. Biochimie 2008;90:1224-32. [DOI: 10.1016/j.biochi.2008.03.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2007] [Accepted: 03/14/2008] [Indexed: 11/15/2022]
6
Cavallari M, Calzolari A, Garbesi A, Di Felice R. Stability and migration of metal ions in G4-wires by molecular dynamics simulations. J Phys Chem B 2007;110:26337-48. [PMID: 17181293 DOI: 10.1021/jp064522y] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
7
Fadrná E, Spacková N, Stefl R, Koca J, Cheatham TE, Sponer J. Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations. Biophys J 2005;87:227-42. [PMID: 15240460 PMCID: PMC1304345 DOI: 10.1529/biophysj.103.034751] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
8
Stefl R, Cheatham TE, Spacková N, Fadrná E, Berger I, Koca J, Sponer J. Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates. Biophys J 2003;85:1787-804. [PMID: 12944293 PMCID: PMC1303352 DOI: 10.1016/s0006-3495(03)74608-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]  Open
9
Giudice E, Lavery R. Simulations of nucleic acids and their complexes. Acc Chem Res 2002;35:350-7. [PMID: 12069619 DOI: 10.1021/ar010023y] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
10
Martínez JM, Elmroth SK, Kloo L. Influence of sodium ions on the dynamics and structure of single-stranded DNA oligomers: a molecular dynamics study. J Am Chem Soc 2001;123:12279-89. [PMID: 11734028 DOI: 10.1021/ja0108786] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
11
Perry PJ, Arnold JR, Jenkins TC. Telomerase inhibitors for the treatment of cancer: the current perspective. Expert Opin Investig Drugs 2001;10:2141-56. [PMID: 11772310 DOI: 10.1517/13543784.10.12.2141] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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