In silico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

(2017) Marek Havrila et al.   Journal of Chemical Theory and Computation

Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field

(2017) Changwon Yang et al.   Journal of Chemical Theory and Computation

Structure of a Stable G-Hairpin

(2017) Martin Gajarský et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies

(2016) Petra Kührová et al.   Journal of Chemical Theory and Computation

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes

(2016) Petr Stadlbauer et al.   Journal of Chemical Theory and Computation

Assessing the Current State of Amber Force Field Modifications for DNA

(2016) Rodrigo Galindo-Murillo et al.   Journal of Chemical Theory and Computation

Free Energy Landscape of GAGA and UUCG RNA Tetraloops

(2016) Sandro Bottaro et al.   Journal of Physical Chemistry Letters

A direct view of the complex multi-pathway folding of telomeric G-quadruplexes

(2016) Mikayel Aznauryan et al.   NUCLEIC ACIDS RESEARCH

Folding and misfolding pathways of G-quadruplex DNA

(2016) Adrien Marchand et al.   NUCLEIC ACIDS RESEARCH

Free-energy landscape of a hyperstable RNA tetraloop

(2016) Jacob C. Miner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advances in RNA molecular dynamics: a simulator's guide to RNA force fields

(2016) Sweta Vangaveti et al.   Wiley Interdisciplinary Reviews-RNA

Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model

(2016) Xiaojun Zeng et al.   Scientific Reports

Involvement of Long-Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G-Quadruplex

(2015) Irene Bessi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Improved Force Field Parameters Lead to a Better Description of RNA Structure

(2015) Christina Bergonzo et al.   Journal of Chemical Theory and Computation

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

A pilgrim's guide to G-quadruplex nucleic acid folding

(2014) Valérie Gabelica   BIOCHIMIE

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

(2014) Petr Stadlbauer et al.   BIOCHIMIE

Unfolding and Conformational Variations of Thrombin-Binding DNA Aptamers: Synthesis, Circular Dichroism and Molecular Dynamics Simulations

(2014) Lidan Sun et al.   ChemMedChem

Folding and Unfolding Pathways of the Human Telomeric G-Quadruplex

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

A Time-Independent Free Energy Estimator for Metadynamics

(2014) Pratyush Tiwary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics

(2014) Fan Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The role of nucleobase interactions in RNA structure and dynamics

(2014) Sandro Bottaro et al.   NUCLEIC ACIDS RESEARCH

G-triplex structure and formation propensity

(2014) Linda Cerofolini et al.   NUCLEIC ACIDS RESEARCH

Well-Tempered Metadynamics Converges Asymptotically

(2014) James F. Dama et al.   PHYSICAL REVIEW LETTERS

A fully atomistic computer simulation study of cold denaturation of a β-hairpin

(2014) Changwon Yang et al.   Nature Communications

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

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures

(2013) Anna Aviñó et al.   FEBS Journal

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

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

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

Kinetic Partitioning Modulates Human Telomere DNA G-Quadruplex Structural Polymorphism

(2013) Xi Long et al.   PLoS One

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA aptamer functionalized nanomaterials for intracellular analysis, cancer cell imaging and drug delivery

(2012) Hang Xing et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Free-Energy Landscape of a Thrombin-Binding DNA Aptamer in Aqueous Environment

(2012) Eunae Kim et al.   Journal of Chemical Theory and Computation

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

Binding properties of human telomeric quadruplex multimers: A new route for drug design

(2011) Annunziata Cummaro et al.   BIOCHIMIE

Quadruplex DNA: A Promising Drug Target for the Medicinal Inorganic Chemist

(2011) Stephen F. Ralph   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Kinetics and Mechanism of Conformational Changes in a G-Quadruplex of Thrombin-Binding Aptamer Induced by Pb2+

(2011) Wei Liu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

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

Multiple Routes to Characterize the Folding of a Small DNA Hairpin

(2010) Guillem Portella et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Metallo-Organic G-Quadruplex Ligands in Anticancer Drug Design

(2010) Y.-L. Jiang et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

The structures of quadruplex nucleic acids and their drug complexes

(2009) Stephen Neidle   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

Heat capacity changes associated with guanine quadruplex formation: An isothermal titration calorimetry study

(2008) Pinaki R. Majhi et al.   BIOPOLYMERS

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

Unfolding Thermodynamics of Intramolecular G-Quadruplexes: Base Sequence Contributions of the Loops†

(2008) Chris M. Olsen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Single-molecule detection of folding and unfolding of the G-quadruplex aptamer in a nanopore nanocavity

(2008) Ji Wook Shim et al.   NUCLEIC ACIDS RESEARCH

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS