Extended molecular dynamics of ac-kitpromoter quadruplex

Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations

(2015) Francesco Di Palma et al.   BMC BIOINFORMATICS

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

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

Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

(2015) Vojtěch Mlýnský et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A New Pathway of DNA G-Quadruplex Formation

(2014) Slavko Čeru et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Direct and Single-Molecule Visualization of the Solution-State Structures of G-Hairpin and G-Triplex Intermediates

(2014) Arivazhagan Rajendran et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

(2014) Petr Stadlbauer et al.   BIOCHIMIE

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

(2014) Konstantinos Gkionis et al.   Journal of Chemical Theory and Computation

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

(2014) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Folding and Unfolding Pathways of the Human Telomeric G-Quadruplex

(2014) Robert D. Gray et al.   JOURNAL OF MOLECULAR BIOLOGY

An Investigation of G-Quadruplex Structural Polymorphism in the Human Telomere Using a Combined Approach of Hydrodynamic Bead Modeling and Molecular Dynamics Simulation

(2014) Huy T. Le et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Multiscale Simulations of Human Telomeric G-Quadruplex DNA

(2014) Matúš Rebič et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

(2014) Jiří Šponer et al.   Journal of Physical Chemistry Letters

Close encounters with DNA

(2014) C Maffeo et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Structure and Conformational Dynamics of a Stacked Dimeric G-Quadruplex Formed by the Human CEB1 Minisatellite

(2014) Michael Adrian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Major G-Quadruplex Formed in the Human BCL-2 Proximal Promoter Adopts a Parallel Structure with a 13-nt Loop in K+ Solution

(2014) Prashansa Agrawal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Structural basis of sodium–potassium exchange of a human telomeric DNA quadruplex without topological conversion

(2014) Zi-Fu Wang et al.   NUCLEIC ACIDS RESEARCH

Flexibility and structural conservation in a c-KIT G-quadruplex

(2014) Dengguo Wei et al.   NUCLEIC ACIDS RESEARCH

Analyzing ion distributions around DNA

(2014) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

G-quadruplex formation in telomeres enhances POT1/TPP1 protection against RPA binding

(2014) S. Ray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Yunqiang Bian et al.   PLoS Computational Biology

The G-Triplex DNA

(2013) Vittorio Limongelli et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

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

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

(2013) Romelia Salomon-Ferrer et al.   Journal of Chemical Theory and Computation

Direct Measurement of Sequential Folding Pathway and Energy Landscape of Human Telomeric G-quadruplex Structures

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

Relative Stability of Different DNA Guanine Quadruplex Stem Topologies Derived Using Large-Scale Quantum-Chemical Computations

(2013) Jiří Šponer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

(2013) Barira Islam et al.   NUCLEIC ACIDS RESEARCH

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

(2013) P. Stadlbauer et al.   NUCLEIC ACIDS RESEARCH

Solution structure of the major G-quadruplex formed in the human VEGF promoter in K+: insights into loop interactions of the parallel G-quadruplexes

(2013) Prashansa Agrawal et al.   NUCLEIC ACIDS RESEARCH

The G-quadruplex ligand, SYUIQ-FM05, targets proto-oncogene c-kittranscription and induces apoptosis in K562 cells

(2013) Fei-Hai Shen et al.   PHARMACEUTICAL BIOLOGY

The critical effect of polarization on the dynamical structure of guanine quadruplex DNA

(2013) Jianing Song et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Structural Dynamics of Human Telomeric G-Quadruplex Loops Studied by Molecular Dynamics Simulations

(2013) Hong Zhu et al.   PLoS One

Conformation and Stability of Intramolecular Telomeric G-Quadruplexes: Sequence Effects in the Loops

(2013) Giovanna Sattin et al.   PLoS One

Synthesis and Evaluation of Quinazolone Derivatives as a New Class of c-KIT G-Quadruplex Binding Ligands

(2013) Xiaoxiao Wang et al.   ACS Medicinal Chemistry Letters

Existence of G-quadruplex structures in promoter region of oncogenes confirmed by G-quadruplex DNA cross-linking strategy

(2013) Libo Yuan et al.   Scientific Reports

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Therapeutic targeting of c-KIT in cancer

(2012) Leonie K Ashman et al.   EXPERT OPINION ON INVESTIGATIONAL DRUGS

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

Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G-Quadruplex DNA Structure

(2012) Parisa Akhshi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unique Structural Features of Interconverting Monomeric and Dimeric G-Quadruplexes Adopted by a Sequence from the Intron of the N-myc Gene

(2012) Marko Trajkovski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Kinetics and Folding Pathways of Intramolecular G-Quadruplex Nucleic Acids

(2012) Amy Y. Q. Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Circular dichroism and guanine quadruplexes

(2012) Michaela Vorlíčková et al.   METHODS

Isothermal folding of G-quadruplexes

(2012) Robert D. Gray et al.   METHODS

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

(2012) Jiří Šponer et al.   METHODS

Small-molecule–induced DNA damage identifies alternative DNA structures in human genes

(2012) Raphaël Rodriguez et al.   Nature Chemical Biology

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Guanine base stacking in G-quadruplex nucleic acids

(2012) Christopher Jacques Lech et al.   NUCLEIC ACIDS RESEARCH

Solution-state structure of an intramolecular G-quadruplex with propeller, diagonal and edgewise loops

(2012) Maja Marušič et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation

(2012) D. Wei et al.   NUCLEIC ACIDS RESEARCH

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

(2012) Claudio A. Morgado et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Stem Cell Factor Receptor/c-Kit: From Basic Science to Clinical Implications

(2012) Johan Lennartsson et al.   PHYSIOLOGICAL REVIEWS

Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”

(2012) Francesca Mocci et al.   Soft Matter

Topological Characterization of Nucleic Acid G-Quadruplexes by UV Absorption and Circular Dichroism

(2011) Andreas Ioannis Karsisiotis et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Linkage of cation binding and folding in human telomeric quadruplex DNA

(2011) Robert D. Gray et al.   BIOPHYSICAL CHEMISTRY

Interactions of Cations with RNA Loop-Loop Complexes

(2011) Abhishek Singh et al.   BIOPHYSICAL JOURNAL

Molecular dynamics simulations and drug discovery

(2011) Jacob D Durrant et al.   BMC BIOLOGY

Treatment of gastrointestinal stromal tumor after imatinib and sunitinib

(2011) Michael Montemurro et al.   CURRENT OPINION IN ONCOLOGY

Inhibition of Cell Proliferation by Quindoline Derivative (SYUIQ-05) through its Preferential Interaction withc-mycPromoter G-Quadruplex

(2011) Tian-Miao Ou et al.   JOURNAL OF MEDICINAL CHEMISTRY

G-Quadruplex-Binding Benzo[a]phenoxazines Down-Regulatec-KITExpression in Human Gastric Carcinoma Cells

(2011) Keith I. E. McLuckie et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis

(2011) Xiaohui Cang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Solution structure of all parallel G-quadruplex formed by the oncogene RET promoter sequence

(2011) Xiaotian Tong et al.   NUCLEIC ACIDS RESEARCH

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process

(2011) Roman V. Reshetnikov et al.   NUCLEIC ACIDS RESEARCH

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

(2011) Xiaohui Cang et al.   NUCLEIC ACIDS RESEARCH

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

Theoretical Perspectives on Protein Folding

(2010) D. Thirumalai et al.   Annual Review of Biophysics

Function of activation loop tyrosine phosphorylation in the mechanism of c-Kit auto-activation and its implication in sunitinib resistance

(2010) J. P. DiNitto et al.   JOURNAL OF BIOCHEMISTRY

New Insights into the Structures of Ligand−Quadruplex Complexes from Molecular Dynamics Simulations

(2010) Jin-Qiang Hou et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Folding Pathways of Human Telomeric Type-1 and Type-2 G-Quadruplex Structures

(2010) Tomoko Mashimo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Hydration Is a Major Determinant of the G-Quadruplex Stability and Conformation of the Human Telomere 3′ Sequence of d(AG3(TTAG3)3)

(2010) M. Clarke Miller et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Disabling c-Myc in Childhood Medulloblastoma and Atypical Teratoid/Rhabdoid Tumor Cells by the Potent G-Quadruplex Interactive Agent S2T1-6OTD

(2010) T. Shalaby et al.   MOLECULAR CANCER THERAPEUTICS

Targeting the c-Kit Promoter G-quadruplexes with 6-Substituted Indenoisoquinolines

(2010) Mallesham Bejugam et al.   ACS Medicinal Chemistry Letters

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

(2009) Mark A. Ditzler et al.   ACCOUNTS OF CHEMICAL RESEARCH

New paradigms in gastrointestinal stromal tumour management

(2009) J.-Y. Blay   ANNALS OF ONCOLOGY

Characterization of a K+-Induced Conformational Switch in a Human Telomeric DNA Oligonucleotide Using 2-Aminopurine Fluorescence

(2009) Robert D. Gray et al.   BIOCHEMISTRY

Anticancer Activity of CX-3543: A Direct Inhibitor of rRNA Biogenesis

(2009) D. Drygin et al.   CANCER RESEARCH

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

Targeting Human Gastrointestinal Stromal Tumor Cells with a Quadruplex-Binding Small Molecule

(2009) Mekala Gunaratnam et al.   JOURNAL OF MEDICINAL CHEMISTRY

Porphyrin Intercalation in G4-DNA Quadruplexes by Molecular Dynamics Simulations

(2009) Manuela Cavallari et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Energetics and Kinetics of a Conformational Switch in G-Quadruplex DNA†

(2009) Robert D. Gray et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The impact of monovalent ion force field model in nucleic acids simulations

(2009) Agnes Noy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Force-induced unfolding of human telomeric G-quadruplex: A steered molecular dynamics simulation study

(2008) Hui Li et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Molecular Dynamics and Principal Components Analysis of Human Telomeric Quadruplex Multimers

(2008) Shozeb Haider et al.   BIOPHYSICAL JOURNAL

Stability and Cations Coordination of DNA and RNA 14-Mer G-Quadruplexes: A Multiscale Computational Approach

(2008) Bruno Pagano 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

Direct NMR Detection of Alkali Metal Ions Bound to G-Quadruplex DNA

(2008) Ramsey Ida et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

G-Quadruplex DNA Assemblies: Loop Length, Cation Identity, and Multimer Formation†

(2008) Nicolas Smargiasso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes

(2008) Niti Kumar et al.   NUCLEIC ACIDS RESEARCH

Stability and kinetics of G-quadruplex structures

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

A Sequence-Independent Study of the Influence of Short Loop Lengths on the Stability and Topology of Intramolecular DNA G-Quadruplexes†

(2007) Anthony Bugaut et al.   BIOCHEMISTRY