Molecular Dynamics Simulations of Dna and Its Complexes

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Progress in Reaction Kinetics and Mechanism

• Publication date

  2004-06-01

• Fields of study

  Biology, Chemistry

• Identifiers
  DOI 10.3184/007967404777726232
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• Cisplatin : chemistry and biochemistry of a leading anticancer drug

  2006cited by this paper
• DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives.

  2004cited by this paper
• A molecular thermodynamic view of DNA-drug interactions: a case study of 25 minor-groove binders.

  2004cited by this paper
• Simulation and modeling of nucleic acid structure, dynamics and interactions.

  2004cited by this paper
• Influence of Spermine on DNA Conformation in a Molecular Dynamics Trajectory of d(CGCGAATTCGCG)2: Major Groove Binding by One Spermine Molecule Delays the A→B Transition

  2004cited by this paper
• Water‐mediated contacts in the trp‐repressor operator complex recognition process

  2004cited by this paper
• Sequence-specific minor groove binding by bis-benzimidazoles: water molecules in ligand recognition.

  2003cited by this paper
• Assessment by molecular dynamics simulations of the structural determinants of DNA-binding specificity for transcription factor Sp1.

  2003cited by this paper
• Simulations of nucleic acids and their complexes.

  2002cited by this paper
• Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: Differential binding of P and M helical enantiomers

  2002cited by this paper
• Interaction between a DNA oligonucleotide and a dinuclear iron(II) supramolecular cylinder; an NMR and molecular dynamics study

  2002cited by this paper
• Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain.

  2002cited by this paper
• Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects.

  2001cited by this paper
• Significance of ligand tails for interaction with the minor groove of B-DNA.

  2001cited by this paper
• Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations.

  2001cited by this paper
• Cooperativity in drug-DNA recognition: a molecular dynamics study.

  2001cited by this paper
• Influence of netropsin's charges on the minor groove width of d(CGCGAATTCGCG)2.

  2001cited by this paper
• Unrestrained 5 ns molecular dynamics simulation of a cisplatin-DNA 1,2-GG adduct provides a rationale for the NMR features and reveals increased conformational flexibility at the platinum binding site.

  2001cited by this paper
• Charge conductivity in peptides: dynamic simulations of a bifunctional model supporting experimental data.

  2000cited by this paper
• Molecular dynamics simulation of hen egg white lysozyme: A test of the GROMOS96 force field against nuclear magnetic resonance data

  2000cited by this paper
• NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex.

  2000cited by this paper
• Binding of distamycin A and netropsin to the 12mer DNA duplexes containing mixed AT.GC sequences with at most five or three successive AT base pairs.

  2000cited by this paper
• Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise *

  2000cited by this paper
• Sequence-specific binding of counterions to B-DNA.

  2000cited by this paper
• All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

  2000cited by this paper
• Molecular modelling of the interaction of carbocyclic analogues of netropsin and distamycin with d(CGCGAATTCGCG)2.

  2000cited by this paper
• Molecular modeling of the intrastrand guanine-guanine DNA adducts produced by cisplatin and oxaliplatin.

  1999cited by this paper
• Molecular Dynamics Study of a Lipid−DNA Complex

  1999cited by this paper
• CALCULATING THE ABSOLUTE FREE ENERGY OF ASSOCIATION OF NETROPSIN AND DNA

  1999cited by this paper
• A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat.

  1999cited by this paper
• Resolving the discrepancies among nucleic acid conformational analyses.

  1999cited by this paper
• Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending.

  1999cited by this paper
• DNA Binding of Ruthenium Tris(1,10-phenanthroline): Evidence for the Dependence of Binding Mode on Metal Complex Concentration.

  1999cited by this paper
• Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC)2: implications for recognition by minor groove binding drugs.

  1999cited by this paper
• The recognition of distorted DNA structures by HMG-D: a footprinting and molecular modelling study.

  1999cited by this paper
• MOLECULAR DYNAMICS SIMULATION OF A ZIF268-DNA COMPLEX IN WATER. SPATIAL PATTERNS AND FLUCTUATIONS SENSED FROM A NANOSECOND TRAJECTORY

  1998cited by this paper
• Targeting the minor groove of DNA.

  1997cited by this paper
• Structure of a nonanucleotide duplex cross-linked by cisplatin at an ApG sequence

  1997cited by this paper
• Localization of Divalent Metal Ions in the Minor Groove of DNA A-Tracts

  1997cited by this paper
• Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA: Fractional Occupancy of Electronegative Pockets

  1997cited by this paper
• Crystallographic insights into DNA minor groove recognition by drugs

  1997cited by this paper
• Design of distamicin analogues to probe the physical origin of the antiparallel side by side oligopeptide binding motif in DNA minor groove recognition.

  1996cited by this paper
• On the sensitivity of MD trajectories to changes in water‐protein interaction parameters: The potato carboxypeptidase inhibitor in water as a test case for the GROMOS force field

  1996cited by this paper
• Calculations of nucleic acid conformations.

  1996cited by this paper
• The electrostatic contribution to the B to Z transition of DNA.

  1996cited by this paper
• Normal mode calculation of a netropsin–DNA complex: Effect of structural deformation on vibrational spectrum

  1995cited by this paper
• Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

  1995cited by this paper
• Crystal structure of double-stranded DNA containing the major adduct of the anticancer drug cisplatin

  1995cited by this paper
• Toward the Accurate Modeling of DNA: The Importance of Long-Range Electrostatics

  1995cited by this paper
• Drug-DNA interactions

  1994cited by this paper
• 1H-NMR of Rh(NH3)4phi3+ Bound to d(TGGCCA)2: Classical Intercalation by a Nonclassical Octahedral Metallointercalator

  1994cited by this paper
• Molecular dynamics studies of DNA

  1994cited by this paper
• Molecular Dynamics Simulations on the Hydration, Structure and Motions of DNA Oligomers

  1993cited by this paper
• Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

  1993cited by this paper
• The basic science of gene therapy.

  1993cited by this paper
• Estimation of absolute and relative entropies of macromolecules using the covariance matrix

  1993cited by this paper
• Force field for platinum binding to adenine

  1993cited by this paper
• What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

  1993cited by this paper
• Isolation and characterization of human cDNA clones encoding a high mobility group box protein that recognizes structural distortions to DNA caused by binding of the anticancer agent cisplatin.

  1992cited by this paper
• A binding mode of lambda-[tris(1,10-phenanthroline)ruthenium(II)]2+ exhibiting preference for purine-3',5'-pyrimidine sites of DNA.

  1991cited by this paper
• Echinomycin binding to alternating AT.

  1991cited by this paper
• Crystal structure of an engrailed homeodomain-DNA complex at 2.8 A resolution: a framework for understanding homeodomain-DNA interactions.

  1990cited by this paper
• ENANTIOPREFERENTIAL DNA-BINDING OF RU-II(1,10-PHENANTHROLINE)3 2+ STUDIED WITH LINEAR AND CIRCULAR-DICHROISM

  1990cited by this paper
• Crystal structure of trp represser/operator complex at atomic resolution

  1988cited by this paper
• Sequence specificity of 125I-labelled Hoechst 33258 damage in six closely related DNA sequences.

  1988cited by this paper
• Sequence specificity of 125I-labelled Hoechst 33258 in intact human cells.

  1988cited by this paper
• Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure.

  1987cited by this paper
• Molecular recognition of B-DNA by Hoechst 33258

  1985cited by this paper
• A critical evaluation of models for complex molecular dynamics: Application to NMR studies of double‐ and single‐stranded DNA

  1983cited by this paper
• Differential stabilization by netropsin of inducible B-like conformations in deoxyribo-, ribo- and 2'-deoxy-2'-fluororibo-adenosine containing duplexes of (dA)n . (dT)n and (dA)n . (dU)na.

  1982cited by this paper
• Die Berechnung optischer und elektrostatischer Gitterpotentiale

  year unknowncited by this paper

• No citing papers are available for this paper.