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

45.5K
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.
45.5K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

20.1K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
20.1K
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

6.0K
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...
6.0K
Newman Projections02:06

Newman Projections

24.2K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
24.2K
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

47.0K
VSEPR Theory for Determination of Electron Pair Geometries
47.0K
Energy Diagrams, Transition States, and Intermediates02:13

Energy Diagrams, Transition States, and Intermediates

22.3K
Free-energy diagrams, or reaction coordinate diagrams, are graphs showing the energy changes that occur during a chemical reaction. The reaction coordinate represented on the horizontal axis shows how far the reaction has progressed structurally. Positions along the x-axis close to the reactants have structures resembling the reactants, while positions close to the products resemble the products.  Peaks on the energy diagram represent stable structures with measurable lifetimes, while...
22.3K

You might also read

Related Articles

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

Sort by
Same author

Ultrasound and microbubble mediated plasmid DNA uptake: A fast, global and multi-mechanisms involved process.

Journal of controlled release : official journal of the Controlled Release Society·2018
Same author

High Hydrostatic Pressure Inducible Trimethylamine <i>N</i>-Oxide Reductase Improves the Pressure Tolerance of Piezosensitive Bacteria <i>Vibrio fluvialis</i>.

Frontiers in microbiology·2018
Same author

Protective role of melatonin in cardiac ischemia-reperfusion injury: From pathogenesis to targeted therapy.

Journal of pineal research·2018
Same author

Poly(Lactide-Co-Glycolide)-Monomethoxy-Poly-(Polyethylene Glycol) Nanoparticles Loaded with Melatonin Protect Adipose-Derived Stem Cells Transplanted in Infarcted Heart Tissue.

Stem cells (Dayton, Ohio)·2018
Same author

Empagliflozin rescues diabetic myocardial microvascular injury via AMPK-mediated inhibition of mitochondrial fission.

Redox biology·2018
Same author

Preparation of Starch-Hard Carbon Spherules from Ginkgo Seeds and Their Phenol-Adsorption Characteristics.

Molecules (Basel, Switzerland)·2018

Related Experiment Video

Updated: Mar 30, 2026

Visualizing Diffusional Dynamics of Gold Nanorods on Cell Membrane using Single Nanoparticle Darkfield Microscopy
09:09

Visualizing Diffusional Dynamics of Gold Nanorods on Cell Membrane using Single Nanoparticle Darkfield Microscopy

Published on: March 5, 2021

4.9K

Visualizing global properties of a molecular dynamics trajectory.

Hao Zhou1, Shangyang Li1, Lee Makowski2,3

  • 1Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts.

Proteins
|November 3, 2015
PubMed
Summary

We developed the sigma-r plot to analyze large molecular dynamics (MD) datasets. This method visualizes protein dynamics, revealing differences across protein classes and effects of mutations.

Keywords:
long MD trajectory datamolecular weightprotein domain structureprotein global dynamicssigma-r plot

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

2.1K

Related Experiment Videos

Last Updated: Mar 30, 2026

Visualizing Diffusional Dynamics of Gold Nanorods on Cell Membrane using Single Nanoparticle Darkfield Microscopy
09:09

Visualizing Diffusional Dynamics of Gold Nanorods on Cell Membrane using Single Nanoparticle Darkfield Microscopy

Published on: March 5, 2021

4.9K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.2K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

2.1K

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Molecular dynamics (MD) trajectories generate vast datasets, posing challenges for understanding protein dynamic behavior.
  • Existing methods for analyzing MD data often lack intuitive representation of global molecular motion.

Purpose of the Study:

  • To introduce a novel method, the sigma-r plot, for simplifying and visualizing global protein dynamics from MD trajectories.
  • To demonstrate the utility of sigma-r plots in characterizing dynamic differences across protein classes and in response to mutations.

Main Methods:

  • The sigma-r plot is generated by plotting the standard deviation of intermolecular distances against the distance itself.
  • Calculations were performed on 10 ns MD trajectories from proteins across four major SCOP fold classes.
  • Analysis included varying simulation times and incorporating single amino acid substitutions.

Main Results:

  • Sigma-r plots revealed distinct dynamic behaviors among different SCOP fold classes.
  • Features in sigma-r plots correlated with protein domain structure, molecular weight, and simulation sampling time.
  • Subtle changes in global dynamics, including those from single amino acid replacements, were detectable.

Conclusions:

  • The sigma-r plot offers a concise, one-dimensional representation of macromolecular global dynamics.
  • This method effectively captures diverse dynamic behaviors and can detect alterations due to structural variations or mutations.
  • Sigma-r plots provide a valuable tool for intuitive analysis of large molecular dynamics datasets.