Molecular dynamics simulations of DNA and its complexes
Molecular dynamics simulations of DNA and its complexes
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA-ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands-including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
b-dna, molecular dynamics, i-125-labeled hoechst-33258, supramolecular cylinder, nucleic acids, crystal-structure, dna-ligand interactions, force-field, molecular recognition, particle mesh ewald, dna, hoechst, nucleic-acids, minor-groove binding, cisplatin, repressor operator complex, major groove, sequence specificity, molecular simulation, netropsin
167-186
Khalid, S.
90fbd954-7248-4f47-9525-4d6af9636394
Rodger, P.M.
1877d68e-9800-4edb-9e6c-8829df27eb49
2004
Khalid, S.
90fbd954-7248-4f47-9525-4d6af9636394
Rodger, P.M.
1877d68e-9800-4edb-9e6c-8829df27eb49
Khalid, S. and Rodger, P.M.
(2004)
Molecular dynamics simulations of DNA and its complexes.
Progress in Reaction Kinetics and Mechanism, 29 (3), .
(doi:10.3184/007967404777726232).
Abstract
This article describes how classical molecular simulation methods are being used to gain a molecular-level understanding of the interaction mechanisms responsible for DNA-ligand recognition, and that govern the response of DNA to ligand binding. Case studies using a variety of different ligands-including small pharmaceutical drugs, proteins and lipids—are used to illustrate the power of modern molecular dynamics simulation methods for understanding how we may control the function and structure of DNA.
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Published date: 2004
Keywords:
b-dna, molecular dynamics, i-125-labeled hoechst-33258, supramolecular cylinder, nucleic acids, crystal-structure, dna-ligand interactions, force-field, molecular recognition, particle mesh ewald, dna, hoechst, nucleic-acids, minor-groove binding, cisplatin, repressor operator complex, major groove, sequence specificity, molecular simulation, netropsin
Identifiers
Local EPrints ID: 54184
URI: http://eprints.soton.ac.uk/id/eprint/54184
ISSN: 1468-6783
PURE UUID: e485eaa4-e99f-44cb-a0bf-6319df33b261
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Date deposited: 05 Aug 2008
Last modified: 16 Mar 2024 03:56
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Author:
S. Khalid
Author:
P.M. Rodger
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