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For: Dolenc J, Gerster S, van Gunsteren WF. Molecular Dynamics Simulations Shed Light on the Enthalpic and Entropic Driving Forces That Govern the Sequence Specific Recognition between Netropsin and DNA. J Phys Chem B 2010;114:11164-72. [DOI: 10.1021/jp100483f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Number Cited by Other Article(s)
1
Mondal S, Bandyopadhyay S. Heterogeneous Dynamical Environment at the Interface of a Protein-DNA Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020;36:4567-4581. [PMID: 32267701 DOI: 10.1021/acs.langmuir.9b03175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
2
Mondal S, Bandyopadhyay S. Flexibility of the Binding Regions of a Protein-DNA Complex and the Structure and Ordering of Interfacial Water. J Chem Inf Model 2019;59:4427-4437. [PMID: 31580657 DOI: 10.1021/acs.jcim.9b00685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
3
Mondal S, Chakraborty K, Bandyopadhyay S. Microscopic understanding of the conformational features of a protein–DNA complex. Phys Chem Chem Phys 2017;19:32459-32472. [DOI: 10.1039/c7cp05161a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
4
Chakraborty K, Bandyopadhyay S. Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules. J Chem Phys 2015;143:045106. [DOI: 10.1063/1.4927568] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
5
Chakraborty K, Bandyopadhyay S. Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers. J Phys Chem B 2015;119:10998-1009. [DOI: 10.1021/acs.jpcb.5b01687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
6
Bruce CD, Ferrara MM, Manka JL, Davis ZS, Register J. Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif. J Mol Recognit 2015;28:325-37. [PMID: 25711379 DOI: 10.1002/jmr.2448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 10/10/2014] [Accepted: 11/09/2014] [Indexed: 12/28/2022]
7
Dršata T, Zgarbová M, Špačková N, Jurečka P, Šponer J, Lankaš F. Mechanical Model of DNA Allostery. J Phys Chem Lett 2014;5:3831-3835. [PMID: 26278756 DOI: 10.1021/jz501826q] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
8
McHarris DM, Barr DA. Truncated variants of the GCN4 transcription activator protein bind DNA with dramatically different dynamical motifs. J Chem Inf Model 2014;54:2869-75. [PMID: 25204850 DOI: 10.1021/ci500448e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
9
Singh M, Sur S, Rastogi GK, Jayaram B, Tandon V. Bi and tri-substituted phenyl rings containing bisbenzimidazoles bind differentially with DNA duplexes: a biophysical and molecular simulation study. MOLECULAR BIOSYSTEMS 2014;9:2541-53. [PMID: 23921527 DOI: 10.1039/c3mb70169g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
10
Petruk AA, Labanda MS, Alvarez RMS, Marti MA. The allosteric modulation of thyroxine-binding globulin affinity is entropy driven. Biochim Biophys Acta Gen Subj 2013;1830:3570-7. [PMID: 23458682 DOI: 10.1016/j.bbagen.2013.02.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 02/20/2013] [Accepted: 02/22/2013] [Indexed: 01/25/2023]
11
Belozerova I, Levicky R. Melting thermodynamics of reversible DNA/ligand complexes at interfaces. J Am Chem Soc 2012;134:18667-76. [PMID: 23046441 PMCID: PMC3498581 DOI: 10.1021/ja3066368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
12
Ferenczy* GG, Keserű* GM. Thermodynamics of Ligand Binding. PHYSICO-CHEMICAL AND COMPUTATIONAL APPROACHES TO DRUG DISCOVERY 2012. [DOI: 10.1039/9781849735377-00023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
13
Sinha SK, Bandyopadhyay S. Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it. J Chem Phys 2012;135:245104. [PMID: 22225189 DOI: 10.1063/1.3670877] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
14
Sinha SK, Bandyopadhyay S. Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations. J Chem Phys 2012;135:135101. [PMID: 21992339 DOI: 10.1063/1.3634004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
15
Assessment of enveloping distribution sampling to calculate relative free enthalpies of binding for eight netropsin-DNA duplex complexes in aqueous solution. J Comput Chem 2012;33:640-51. [DOI: 10.1002/jcc.22879] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2011] [Accepted: 10/28/2011] [Indexed: 12/25/2022]
16
Chakravarty AR, Roy M. Photoactivated DNA Cleavage and Anticancer Activity of 3d Metal Complexes. PROGRESS IN INORGANIC CHEMISTRY 2011. [DOI: 10.1002/9781118148235.ch3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
17
Choutko A, van Gunsteren WF, Hünenberger PH. Preferential Affinity of the Components of Liquid Mixtures at a Rigid Non-Polar Surface: Enthalpic and Entropic Driving Forces. Chemphyschem 2011;12:3214-23. [DOI: 10.1002/cphc.201100541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Indexed: 01/01/2023]
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