Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...

You might also read

Related Articles

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

Sort by
Same author

Strand Displacement Increases the Fidelity of DNA Polymerases.

Biochemistry·2026
Same author

Probing Electrostatics in a DNA Repair Enzyme with a pH-Sensitive Nitroxyl Spin Label.

The journal of physical chemistry. B·2026
Same author

Usnic Acid Derivatives as Inhibitors of <i>Mycobacterium tuberculosis</i> Uracil-DNA Glycosylase.

International journal of molecular sciences·2026
Same author

Peptide Modulator of TRPV1 Channel Increases Long-Term Potentiation in the Hippocampus and Reduces Anxiety and Fear in Mice Under Acute Stress.

Marine drugs·2026
Same author

8-Oxoguanine: A Lesion, an Epigenetic Mark, or a Molecular Signal?

International journal of molecular sciences·2025
Same author

Uracil-DNA Glycosylase from <i>Beta vulgaris</i>: Properties and Response to Abiotic Stress.

International journal of molecular sciences·2025

Related Experiment Video

Updated: May 17, 2026

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

MDTRA: a molecular dynamics trajectory analyzer with a graphical user interface.

Alexander V Popov1, Yury N Vorobjev, Dmitry O Zharkov

  • 1SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia. apopov@niboch.nsc.ru.

Journal of Computational Chemistry
|October 11, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces MD Trajectory Reader and Analyzer (MDTRA), an open-source program simplifying molecular dynamics (MD) simulation analysis with a graphical interface. MDTRA facilitates result visualization and analysis for researchers, including DNA repair enzyme studies.

More Related Videos

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Related Experiment Videos

Last Updated: May 17, 2026

New Features in Visual Dynamics 3.0
05:00

New Features in Visual Dynamics 3.0

Published on: August 9, 2024

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
06:37

Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package

Published on: September 17, 2021

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Existing molecular dynamics (MD) analysis tools often rely on command-line interfaces, posing a barrier for researchers without programming expertise.
  • There is a need for user-friendly software to streamline the analysis and visualization of complex MD simulation data.

Purpose of the Study:

  • To introduce MD Trajectory Reader and Analyzer (MDTRA), an open-source, cross-platform program designed for intuitive MD simulation analysis.
  • To provide researchers with a graphical user interface (GUI) for efficient exploration and visualization of MD results.
  • To offer a versatile tool capable of handling various trajectory formats and performing diverse analytical tasks.

Main Methods:

  • Development of an open-source, cross-platform application with a graphical user interface (GUI).
  • Implementation of tools to handle trajectories in Protein Data Bank (PDB) file sets and convert other formats.
  • Integration of analysis modules for parameters such as interatomic distances, angles, root-mean-square deviation (RMSD), and solvent-accessible surface area (SASA).

Main Results:

  • MDTRA offers a user-friendly GUI, simplifying complex MD data analysis and visualization.
  • The software supports trajectories as PDB file sets and includes conversion utilities for other formats.
  • MDTRA analyzes key parameters including distances, angles, dihedral angles, RMSD, and SASA.

Conclusions:

  • MDTRA significantly enhances the accessibility and efficiency of molecular dynamics simulation analysis for researchers.
  • The program's GUI and comprehensive analysis tools facilitate the interpretation of simulation results.
  • MDTRA's application to the analysis of formamidopyrimidine-DNA glycosylase MD simulations demonstrates its utility in studying DNA repair enzymes.