Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Oct 21, 2025

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes.

Na Li¹, Ya Gao², Feng Qiu³

¹Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.

Molecules (Basel, Switzerland)

|September 10, 2021

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Nine pairs of megastigmane enantiomers from the leaves of Eucommia ulmoides Oliver.

Journal of natural medicines·2017

Same author

Impact of the Publication of Appropriate Use Criteria on Utilization Rates of Myocardial Perfusion Imaging Studies in Ontario, Canada: A Population-Based Study.

Journal of the American Heart Association·2017

Same author

Stress testing after percutaneous coronary interventions: a population-based study.

CMAJ open·2017

Same author

Metabolic profiling of quercetin in rats using ultra-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry.

Biomedical chromatography : BMC·2017

Same author

[Resiquimod (R848) has more stronger immune adjuvantivity than other tested TLR agonists].

Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology·2017

Same author

Oxyresveratrol Is a Phytoestrogen Exerting Anti-inflammatory Effects Through NF-κB and Estrogen Receptor Signaling.

Inflammation·2017

The Drude force field shows the best performance for molecular dynamics simulations of G-quadruplexes, offering superior structural and stability insights for anti-cancer drug development and material science applications.

Area of Science:

Biophysics
Computational Chemistry
Structural Biology

Background:

G-quadruplexes (GQs) are crucial in cancer research and material science.
Molecular dynamics (MD) simulations are vital for understanding GQ structure-function relationships.

Purpose of the Study:

To systematically benchmark five leading force fields for MD simulations of GQs.
To evaluate force field performance in key aspects of GQ structure and dynamics.

Main Methods:

Comparative analysis of parmbsc0, parmbsc1, OL15, AMOEBA, and Drude2017 force fields.
MD simulations focused on GQ structural stability, ion channel dynamics, Hoogsteen hydrogen bonds, and backbone dihedral angles.

Main Results:

The Drude force field demonstrated superior overall performance across all evaluated metrics.

Keywords:

G-Quadruplex force field molecular dynamics simulation polarization effect

More Related Videos

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

Related Experiment Videos

Last Updated: Oct 21, 2025

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers

Published on: September 19, 2017

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Author Spotlight: Characterizing DNA G-Quadruplex by Bis-3-Chloropiperidine Based Chemical Mapping

Published on: May 12, 2023

While exhibiting potential over-polarization, Drude force field provided the most accurate simulations.

Other force fields showed varying degrees of success in specific aspects.

Conclusions:

The Drude force field is the recommended choice for accurate MD simulations of G-quadruplexes.
This finding aids in advancing GQ-targeted therapies and novel material design.