Research graph
References from Impact of Intercalators on the Properties of DNA Analyzed by Molecular Dynamics Simulations. Local targets link to admitted publications; unresolved targets remain external evidence.
Stacking interactions and intercalative DNA binding
10.1006/meth.1998.0584 · 1998 · External reference
Doxorubicin and other anthracyclines in cancers: Activity, chemoresistance and its overcoming
10.1016/j.mam.2023.101205 · 2023 · External reference
New insights into the activities and toxicities of the old anticancer drug doxorubicin
10.1111/febs.15583 · 2021 · External reference
Intercalation processes of copper complexes in DNA
10.1093/nar/gkv467 · 2015 · External reference
Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations
10.1016/j.jmgm.2012.05.006 · 2012 · External reference
Insertion of a bulky rhodium complex into a DNA cytosine-cytosine mismatch: an NMR solution study
10.1021/ja0739436 · 2007 · External reference
Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs
10.1093/nar/gkq597 · 2010 · External reference
DNA-doxorubicin interaction: New insights and peculiarities
10.1002/bip.22998 · 2017 · External reference
The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics
10.1038/ncomms8304 · 2015 · External reference
Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold
10.1093/nar/gkab265 · 2021 · External reference
Effect of YOYO-1 on the mechanical properties of DNA
10.1039/c4sm02025a · 2014 · External reference
Mechanical and structural properties of YOYO-1 complexed DNA
10.1093/nar/gkq434 · 2010 · External reference
Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations
10.1093/nar/gkab143 · 2021 · External reference
Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes
10.1063/1.5117163 · 2019 · External reference
On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes
10.1021/ja8001666 · 2008 · External reference
Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA
10.1021/ja301649k · 2012 · External reference
Cooperative effects on the formation of intercalation sites
10.1093/nar/gkh788 · 2004 · External reference
Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects
10.1021/acs.jpcb.0c05840 · 2020 · External reference
Molecular mechanism and binding free energy of doxorubicin intercalation in DNA
10.1039/c8cp06776g · 2019 · External reference
Automatic atom type and bond type perception in molecular mechanical calculations
10.1016/j.jmgm.2005.12.005 · 2006 · External reference
Development and testing of a general amber force field
10.1002/jcc.20035 · 2004 · External reference
Unresolved reference
External reference
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
10.1021/j100142a004 · 1993 · External reference
AmberTools
10.1021/acs.jcim.3c01153 · 2023 · External reference
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
10.1016/j.bbagen.2014.09.007 · 2015 · External reference
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy
10.1021/bi00027a004 · 1995 · External reference
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
10.1002/wcms.1220 · 2015 · External reference
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
10.1002/jcc.24874 · 2017 · External reference
Parmbsc1: a refined force field for DNA simulations
10.1038/nmeth.3658 · 2016 · External reference
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
10.1021/jp8001614 · 2008 · External reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · 1983 · External reference
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
10.1063/1.464397 · 1993 · External reference
A smooth particle mesh Ewald method
10.1063/1.470117 · 1995 · External reference
Canonical sampling through velocity rescaling
10.1063/1.2408420 · 2007 · External reference
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
10.1063/1.3073889 · 2009 · External reference
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
10.1016/0021-9991(77)90098-5 · 1977 · External reference
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
10.1016/0021-9991(83)90014-1 · 1983 · External reference
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
10.1002/jcc.540130805 · 1992 · External reference
Adaptively biased molecular dynamics of free energy calculations
10.1063/1.2844595 · 2008 · External reference
The weighted histogram analysis method for free energy calculations on biomolecules. I. The method
10.1002/jcc.540130812 · 1992 · External reference
Free Energy Landscape of H2A-H2B Displacement From Nucleosome
10.1016/j.jmb.2022.167707 · 2022 · External reference
Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance Matrix
10.1016/0009-2614(93)89366-p · 1993 · External reference
Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA
10.1073/pnas.2020452118 · 2021 · External reference
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
10.1093/nar/gkg680 · 2003 · External reference
Stiff Chains and Filaments under Tension
10.1021/ma00124a044 · 1995 · External reference
Elasticity of DNA and the effect of dendrimer binding
10.1140/epje/i2013-13068-1 · 2013 · External reference
DNA Elasticity from Short DNA to Nucleosomal DNA
10.1021/acs.jpcb.5b03006 · 2015 · External reference
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
10.1021/jp961992r · 1997 · External reference
Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment
10.1021/ct501170h · 2015 · External reference
Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations
10.1002/prot.25077 · 2016 · External reference
Designer Catalyst-Enabled Regiodivergent Histone Acetylation
10.1021/jacs.5c01699 · 2025 · External reference
A polarized view on DNA under tension
10.1063/1.5004019 · 2018 · External reference
Bubble nucleation and cooperativity in DNA melting
10.1016/j.jmb.2004.02.072 · 2004 · External reference
Ionic effects on the elasticity of single DNA molecules
10.1073/pnas.94.12.6185 · 1997 · External reference
Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin
10.1021/bi00462a016 · 1990 · External reference
Induction of stable transcriptional blockage sites by adriamycin: GpC specificity of apparent adriamycin-DNA adducts and dependence on iron(III) ions
10.1021/bi00475a032 · 1990 · External reference
Deoxyribonucleic acid binding studies on several new anthracycline antitumor antibiotics. Sequence preference and structure-activity relationships of marcellomycin and its analogues as compared to adriamycin
10.1021/bi00585a028 · 1979 · External reference
New insights into the mechanism of the DNA/doxorubicin interaction
10.1021/jp411429g · 2014 · External reference
Interaction of doxorubicin with polynucleotides. A spectroscopic study
10.1021/bi401687v · 2014 · External reference
Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides
10.1093/nar/26.20.4721 · 1998 · External reference
The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA
10.1016/j.bbrc.2010.11.015 · 2010 · External reference
Kinetic studies of anthracycline-DNA interaction by fluorescence stopped flow confirm a complex association mechanism
10.1021/bi00427a038 · 1989 · External reference
Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
10.1093/nar/gkf409 · 2002 · External reference
Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
10.1093/nar/gkv087 · 2015 · External reference
Characterization of the Binding of the Fluorescent Dyes YO and YOYO to DNA by Polarized Light Spectroscopy
10.1021/ja00098a004 · 1994 · External reference
Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
10.3390/molecules26123748 · 2021 · External reference
DNA-doxorubicin interaction: New insights and peculiarities
10.1002/bip.22998 · ExternalCitation · doi-reference
Development and testing of a general amber force field
10.1002/jcc.20035 · ExternalCitation · doi-reference
GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms
10.1002/jcc.24874 · ExternalCitation · doi-reference
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
10.1002/jcc.540130805 · ExternalCitation · doi-reference
The weighted histogram analysis method for free energy calculations on biomolecules. I. The method
10.1002/jcc.540130812 · ExternalCitation · doi-reference
Mechanism for verification of mismatched and homoduplex DNAs by nucleotides-bound MutS analyzed by molecular dynamics simulations
10.1002/prot.25077 · ExternalCitation · doi-reference
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
10.1002/wcms.1220 · ExternalCitation · doi-reference
Stacking interactions and intercalative DNA binding
10.1006/meth.1998.0584 · ExternalCitation · doi-reference
Estimation of Absolute and Relative Entropies of Macromolecules Using the Covariance Matrix
10.1016/0009-2614(93)89366-p · ExternalCitation · doi-reference
Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
10.1016/0021-9991(77)90098-5 · ExternalCitation · doi-reference
Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations
10.1016/0021-9991(83)90014-1 · ExternalCitation · doi-reference
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)
10.1016/j.bbagen.2014.09.007 · ExternalCitation · doi-reference
The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA
10.1016/j.bbrc.2010.11.015 · ExternalCitation · doi-reference
Bubble nucleation and cooperativity in DNA melting
10.1016/j.jmb.2004.02.072 · ExternalCitation · doi-reference
Free Energy Landscape of H2A-H2B Displacement From Nucleosome
10.1016/j.jmb.2022.167707 · ExternalCitation · doi-reference
Automatic atom type and bond type perception in molecular mechanical calculations
10.1016/j.jmgm.2005.12.005 · ExternalCitation · doi-reference
Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations
10.1016/j.jmgm.2012.05.006 · ExternalCitation · doi-reference
Doxorubicin and other anthracyclines in cancers: Activity, chemoresistance and its overcoming
10.1016/j.mam.2023.101205 · ExternalCitation · doi-reference
AmberTools
10.1021/acs.jcim.3c01153 · ExternalCitation · doi-reference
Thermodynamic Dissection of the Intercalation Binding Process of Doxorubicin to dsDNA with Implications of Ionic and Solvent Effects
10.1021/acs.jpcb.0c05840 · ExternalCitation · doi-reference
DNA Elasticity from Short DNA to Nucleosomal DNA
10.1021/acs.jpcb.5b03006 · ExternalCitation · doi-reference
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy
10.1021/bi00027a004 · ExternalCitation · doi-reference
Kinetic studies of anthracycline-DNA interaction by fluorescence stopped flow confirm a complex association mechanism
10.1021/bi00427a038 · ExternalCitation · doi-reference
Structural comparison of anticancer drug-DNA complexes: adriamycin and daunomycin
10.1021/bi00462a016 · ExternalCitation · doi-reference
Induction of stable transcriptional blockage sites by adriamycin: GpC specificity of apparent adriamycin-DNA adducts and dependence on iron(III) ions
10.1021/bi00475a032 · ExternalCitation · doi-reference
Deoxyribonucleic acid binding studies on several new anthracycline antitumor antibiotics. Sequence preference and structure-activity relationships of marcellomycin and its analogues as compared to adriamycin
10.1021/bi00585a028 · ExternalCitation · doi-reference
Interaction of doxorubicin with polynucleotides. A spectroscopic study
10.1021/bi401687v · ExternalCitation · doi-reference
Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment
10.1021/ct501170h · ExternalCitation · doi-reference
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
10.1021/j100142a004 · ExternalCitation · doi-reference
Characterization of the Binding of the Fluorescent Dyes YO and YOYO to DNA by Polarized Light Spectroscopy
10.1021/ja00098a004 · ExternalCitation · doi-reference
Insertion of a bulky rhodium complex into a DNA cytosine-cytosine mismatch: an NMR solution study
10.1021/ja0739436 · ExternalCitation · doi-reference
Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA
10.1021/ja301649k · ExternalCitation · doi-reference
On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes
10.1021/ja8001666 · ExternalCitation · doi-reference
Designer Catalyst-Enabled Regiodivergent Histone Acetylation
10.1021/jacs.5c01699 · ExternalCitation · doi-reference
New insights into the mechanism of the DNA/doxorubicin interaction
10.1021/jp411429g · ExternalCitation · doi-reference
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
10.1021/jp8001614 · ExternalCitation · doi-reference
The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii
10.1021/jp961992r · ExternalCitation · doi-reference
Stiff Chains and Filaments under Tension
10.1021/ma00124a044 · ExternalCitation · doi-reference
The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics
10.1038/ncomms8304 · ExternalCitation · doi-reference
Parmbsc1: a refined force field for DNA simulations
10.1038/nmeth.3658 · ExternalCitation · doi-reference
Effect of YOYO-1 on the mechanical properties of DNA
10.1039/c4sm02025a · ExternalCitation · doi-reference
Molecular mechanism and binding free energy of doxorubicin intercalation in DNA
10.1039/c8cp06776g · ExternalCitation · doi-reference
Canonical sampling through velocity rescaling
10.1063/1.2408420 · ExternalCitation · doi-reference
Adaptively biased molecular dynamics of free energy calculations
10.1063/1.2844595 · ExternalCitation · doi-reference
Isothermal-isobaric molecular dynamics using stochastic velocity rescaling
10.1063/1.3073889 · ExternalCitation · doi-reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · ExternalCitation · doi-reference
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
10.1063/1.464397 · ExternalCitation · doi-reference
A smooth particle mesh Ewald method
10.1063/1.470117 · ExternalCitation · doi-reference
A polarized view on DNA under tension
10.1063/1.5004019 · ExternalCitation · doi-reference
Understanding enhanced mechanical stability of DNA in the presence of intercalated anticancer drug: Implications for DNA associated processes
10.1063/1.5117163 · ExternalCitation · doi-reference
Torsional stress can regulate the unwrapping of two outer half superhelical turns of nucleosomal DNA
10.1073/pnas.2020452118 · ExternalCitation · doi-reference
Ionic effects on the elasticity of single DNA molecules
10.1073/pnas.94.12.6185 · ExternalCitation · doi-reference
Identification and hydropathic characterization of structural features affecting sequence specificity for doxorubicin intercalation into DNA double-stranded polynucleotides
10.1093/nar/26.20.4721 · ExternalCitation · doi-reference
Ethidium bromide interactions with DNA: an exploration of a classic DNA-ligand complex with unbiased molecular dynamics simulations
10.1093/nar/gkab143 · ExternalCitation · doi-reference
Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold
10.1093/nar/gkab265 · ExternalCitation · doi-reference
Structural perturbations in DNA caused by bis-intercalation of ditercalinium visualised by atomic force microscopy
10.1093/nar/gkf409 · ExternalCitation · doi-reference
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
10.1093/nar/gkg680 · ExternalCitation · doi-reference
Cooperative effects on the formation of intercalation sites
10.1093/nar/gkh788 · ExternalCitation · doi-reference
Mechanical and structural properties of YOYO-1 complexed DNA
10.1093/nar/gkq434 · ExternalCitation · doi-reference
Magnetic tweezers measurements of the nanomechanical properties of DNA in the presence of drugs
10.1093/nar/gkq597 · ExternalCitation · doi-reference
Single-molecule kinetics and footprinting of DNA bis-intercalation: the paradigmatic case of Thiocoraline
10.1093/nar/gkv087 · ExternalCitation · doi-reference
Intercalation processes of copper complexes in DNA
10.1093/nar/gkv467 · ExternalCitation · doi-reference
New insights into the activities and toxicities of the old anticancer drug doxorubicin
10.1111/febs.15583 · ExternalCitation · doi-reference
Elasticity of DNA and the effect of dendrimer binding
10.1140/epje/i2013-13068-1 · ExternalCitation · doi-reference
Two Intercalation Mechanisms of Oxazole Yellow Dimer (YOYO-1) into DNA
10.3390/molecules26123748 · ExternalCitation · doi-reference
