Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

(2015) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

All-Atomic Simulations on Human Telomeric G-Quadruplex DNA Binding with Thioflavin T

(2015) Di Luo et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes

(2015) Jenifer Rubio-Magnieto et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

(2015) Stephan A Ohnmacht et al.   Scientific Reports

Small-molecule quadruplex-targeted drug discovery

(2014) Stephan A. Ohnmacht et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Association of G-quadruplex forming sequences with human mtDNA deletion breakpoints

(2014) Dawei W Dong et al.   BMC GENOMICS

G-quadruplex ligands: Mechanisms of anticancer action and target binding

(2014) N. S. Ilyinsky et al.   MOLECULAR BIOLOGY

Mechanistic insight into ligand binding to G-quadruplex DNA

(2014) Francesco Saverio Di Leva et al.   NUCLEIC ACIDS RESEARCH

Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set

(2014) Huiyong Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Elevated Levels of G-Quadruplex Formation in Human Stomach and Liver Cancer Tissues

(2014) Giulia Biffi et al.   PLoS One

DNA G-quadruplex and its potential as anticancer drug target

(2014) Buket Onel et al.   Science China-Chemistry

Atomistic Picture for the Folding Pathway of a Hybrid-1 Type Human Telomeric DNA G-quadruplex

(2014) Yunqiang Bian et al.   PLoS Computational Biology

G-quadruplex interacting small molecules and drugs: from bench toward bedside

(2014) Sebastian Müller et al.   Expert Review of Clinical Pharmacology

Relevance of G-quadruplex structures to pharmacogenetics

(2014) Simone L. Cree et al.   Frontiers in Pharmacology

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

(2013) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models

(2013) Lei Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crystal Structure of a Promoter Sequence in the B-raf Gene Reveals an Intertwined Dimer Quadruplex

(2013) Dengguo Wei et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Solution Structure of an Intramolecular (3 + 1) Human Telomeric G-Quadruplex Bound to a Telomestatin Derivative

(2013) Wan Jun Chung et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

(2013) M. Nambiar et al.   MOLECULAR AND CELLULAR BIOLOGY

G-Quadruplexes as Potential Therapeutic Targets for Embryonal Tumors

(2013) Tarek Shalaby et al.   MOLECULES

Potential G-quadruplex formation at breakpoint regions of chromosomal translocations in cancer may explain their fragility

(2012) Vijeth K. Katapadi et al.   GENOMICS

Intercalation of Daunomycin into Stacked DNA Base Pairs. DFT Study of an Anticancer Drug

(2012) Giampaolo Barone et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

G-quadruplexes: targets and tools in anticancer drug design

(2012) Markus Düchler   JOURNAL OF DRUG TARGETING

Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations

(2012) Hongxing Lei et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Multistep Drug Intercalation: Molecular Dynamics and Free Energy Studies of the Binding of Daunomycin to DNA

(2012) Matthieu Wilhelm et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

(2012) Jiří Šponer et al.   METHODS

A structural analysis of G-quadruplex/ligand interactions

(2011) Shozeb M. Haider et al.   BIOCHIMIE

Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?

(2011) Shankar Balasubramanian et al.   NATURE REVIEWS DRUG DISCOVERY

Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations

(2010) Tingjun Hou et al.   Journal of Chemical Information and Modeling

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

(2010) Tingjun Hou et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural and Conformational Requisites in DNA Quadruplex Groove Binding: Another Piece to the Puzzle

(2010) Sandro Cosconati et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Spectroscopy Probing of the Formation, Recognition, and Conversion of a G-Quadruplex in the Promoter Region of thebcl-2Oncogene

(2009) Huihui Li et al.   CHEMISTRY-A EUROPEAN JOURNAL

Targeting G-Quadruplex DNA with Small Molecules

(2009) Nathan W. Luedtke   CHIMIA

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

(2009) Eva Fadrná et al.   Journal of Chemical Theory and Computation

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

(2009) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Energetics of the Human Tel-22 Quadruplex−Telomestatin Interaction: A Molecular Dynamics Study

(2008) Saurabh Agrawal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the Molecular Mechanism of Drug Intercalation into DNA: A Simulation Study of the Intercalation Pathway, Free Energy, and DNA Structural Changes

(2008) Arnab Mukherjee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural Basis of DNA Quadruplex Recognition by an Acridine Drug

(2008) Nancy H. Campbell et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dissociation of minor groove binders from DNA: insights from metadynamics simulations

(2008) A. V. Vargiu et al.   NUCLEIC ACIDS RESEARCH

Stability and kinetics of G-quadruplex structures

(2008) A. N. Lane et al.   NUCLEIC ACIDS RESEARCH