Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies

(2017) Haohao Fu et al.   Journal of Chemical Theory and Computation

Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates

(2017) François Dehez et al.   NUCLEIC ACIDS RESEARCH

Ibuprofen and ketoprofen potentiate UVA-induced cell death by a photosensitization process

(2017) Emmanuelle Bignon et al.   Scientific Reports

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

(2016) Roberto Improta et al.   CHEMICAL REVIEWS

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations

(2016) Haohao Fu et al.   Journal of Chemical Theory and Computation

Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method

(2016) Adrien Lesage et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Cyclobutane Thymine Photodimerization Mechanism Revealed by Nonadiabatic Molecular Dynamics

(2016) Clemens Rauer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Two-photon-absorption DNA sensitization via solvated electron production: unraveling photochemical pathways by molecular modeling and simulation

(2016) Hugo Gattuso et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Hydrogen abstraction by photoexcited benzophenone: consequences for DNA photosensitization

(2016) Marco Marazzi et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations

(2016) Hugo Gattuso et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

From non-covalent binding to irreversible DNA lesions: nile blue and nile red as photosensitizing agents

(2016) Hugo Gattuso et al.   Scientific Reports

Enhancing Intersystem Crossing in Phenotiazinium Dyes by Intercalation into DNA

(2015) Juan J. Nogueira et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5-Methyl-2-pyrimidone Deoxyribonucleoside

(2015) Emmanuelle Bignon et al.   CHEMISTRY-A EUROPEAN JOURNAL

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

(2015) Samuel Genheden et al.   Expert Opinion on Drug Discovery

Effective Two-Photon Excited Photodynamic Therapy of Xenograft Tumors Sensitized by Water-Soluble Bis(arylidene)cycloalkanone Photosensitizers

(2015) Qianli Zou et al.   JOURNAL OF MEDICINAL CHEMISTRY

Resolving the Benzophenone DNA-Photosensitization Mechanism at QM/MM Level

(2015) Elise Dumont et al.   Journal of Physical Chemistry Letters

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Understanding DNA under oxidative stress and sensitization: the role of molecular modeling

(2015) Elise Dumont et al.   Frontiers in Chemistry

Stress-induced DNA damage biomarkers: applications and limitations

(2015) Zacharenia Nikitaki et al.   Frontiers in Chemistry

Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology

(2015) Hugo Gattuso et al.   Frontiers in Chemistry

Photophysical Properties of Ruthenium(II) Polypyridyl DNA Intercalators: Effects of the Molecular Surroundings Investigated by Theory

(2014) Thibaut Véry et al.   CHEMISTRY-A EUROPEAN JOURNAL

Increased mutability and decreased repairability of a three-lesion clustered DNA-damaged site comprised of an AP site and bi-stranded 8-oxoG lesions

(2014) Siobhan Cunniffe et al.   INTERNATIONAL JOURNAL OF RADIATION BIOLOGY

Interaction of Palmatine with DNA: An Environmentally Controlled Phototherapy Drug

(2014) Élise Dumont et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Oxidatively Generated Damage to Cellular DNA by UVB and UVA Radiation,

(2014) Jean Cadet et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Photosensitization of DNA by 5-Methyl-2-Pyrimidone Deoxyribonucleoside: (6-4) Photoproduct as a Possible Trojan Horse

(2013) Victoria Vendrell-Criado et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular Basis for Sequence-Dependent Induced DNA Bending

(2013) Michael Rettig et al.   CHEMBIOCHEM

Theoretical evidence of photo-induced charge transfer from DNA to intercalated ruthenium (II) organometallic complexes

(2013) Agisilaos Chantzis et al.   CHEMICAL PHYSICS LETTERS

Biological Consequences of Radiation-induced DNA Damage: Relevance to Radiotherapy

(2013) M.E. Lomax et al.   CLINICAL ONCOLOGY

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

(2013) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Overcoming dissipation in the calculation of standard binding free energies by ligand extraction

(2013) Camilo Velez-Vega et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks

(2013) Emilie Cauët et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Benzophenone and DNA: Evidence for a Double Insertion Mode and Its Spectral Signature

(2013) Elise Dumont et al.   Journal of Physical Chemistry Letters

Replication fork collapse is a major cause of the high mutation frequency at three-base lesion clusters

(2013) Yuliya Sedletska et al.   NUCLEIC ACIDS RESEARCH

DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation

(2013) J. Cadet et al.   Cold Spring Harbor Perspectives in Biology

Theoretical Modeling of Large Molecular Systems. Advances in the Local Self Consistent Field Method for Mixed Quantum Mechanics/Molecular Mechanics Calculations

(2012) Antonio Monari et al.   ACCOUNTS OF CHEMICAL RESEARCH

Benzophenone Photosensitized DNA Damage

(2012) M. Consuelo Cuquerella et al.   ACCOUNTS OF CHEMICAL RESEARCH

Biological consequences of formation and repair of complex DNA damage

(2012) Karin Magnander et al.   CANCER LETTERS

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

(2012) James C. Gumbart et al.   Journal of Chemical Theory and Computation

Photoinduced Damage to Cellular DNA: Direct and Photosensitized Reactions†

(2012) Jean Cadet et al.   PHOTOCHEMISTRY AND PHOTOBIOLOGY

Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)2]2+

(2012) Thibaut Very et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Complexity in the binding of minor groove agents: netropsin has two thermodynamically different DNA binding modes at a single site

(2011) Edwin A. Lewis et al.   NUCLEIC ACIDS RESEARCH

DNA damage spectra induced by photosensitization

(2011) Bernd Epe   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

DNA/RNA: Building Blocks of Life Under UV Irradiation

(2010) Thomas Gustavsson et al.   Journal of Physical Chemistry Letters

Delayed repair of radiation induced clustered DNA damage: Friend or foe?

(2010) Laura J. Eccles et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Clustered DNA lesion repair in eukaryotes: Relevance to mutagenesis and cell survival

(2010) Evelyne Sage et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

The Yield, Processing, and Biological Consequences of Clustered DNA Damage Induced by Ionizing Radiation

(2009) Naoya SHIKAZONO et al.   JOURNAL OF RADIATION RESEARCH

Conformational analysis of nucleic acids revisited: Curves+

(2009) R. Lavery et al.   NUCLEIC ACIDS RESEARCH

A detailed binding free energy study of 2 : 1 ligand–DNA complex formation by experiment and simulation

(2009) Witcha Treesuwan et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Oxidative Stress and Oxidative Damage in Carcinogenesis

(2009) James E. Klaunig et al.   TOXICOLOGIC PATHOLOGY

Sequence Dependent Ultrafast Electron Transfer of Nile Blue in Oligonucleotides

(2008) Rajib Kumar Mitra et al.   JOURNAL OF FLUORESCENCE