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

Orthogonal Trajectories01:26

Orthogonal Trajectories

61
Orthogonal trajectories describe the geometric relationship between two families of curves that intersect each other at right angles. One illustrative case involves a family of parabolas that open sideways along the x-axis. These curves share a common shape but differ by a scaling parameter, resulting in a set of curves that all pass through the origin and widen at different rates.Determining Orthogonal TrajectoriesTo identify the orthogonal trajectories for these parabolas, the first step...
61
Causes of Similarity-Dissimilarity Effect01:26

Causes of Similarity-Dissimilarity Effect

261
The similarity-dissimilarity effect, a fundamental concept in social psychology, explains how interpersonal similarities and differences influence attraction and social interactions. This effect is supported by three key psychological perspectives: balance theory, social comparison theory, and consensual validation.Balance Theory and Cognitive ConsistencyBalance theory, developed by Fritz Heider, posits that individuals seek cognitive consistency in their relationships. When two people share...
261
Statistical Significance01:50

Statistical Significance

21.8K
Once data is collected from both the experimental and the control groups, a statistical analysis is conducted to find out if there are meaningful differences between the two groups. A statistical analysis determines how likely any difference found is due to chance (and thus not meaningful). In psychology, group differences are considered meaningful, or significant, if the odds that these differences occurred by chance alone are 5 percent or less. Stated another way, if we repeated this...
21.8K
Factors Influencing Attraction III: Similarity01:23

Factors Influencing Attraction III: Similarity

760
The similarity hypothesis suggests that individuals are more likely to form relationships with others who share similar attitudes, beliefs, values, and interests. This concept has been widely studied in social psychology, demonstrating that perceived similarity fosters interpersonal attraction. In an experiment supporting this hypothesis, participants were presented with fabricated information indicating that strangers held attitudes similar to their own. The results showed that participants...
760
Molecular Models02:00

Molecular Models

43.7K
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.
43.7K
Probability in Statistics01:14

Probability in Statistics

23.4K
Probability is the likelihood of an event occurring. The term event is defined as a collection of results of a procedure. An event is a simple event when an outcome cannot be divided into simpler parts.
An example of a simple event is a coin toss. The result of a coin toss is either a head or a tail. Here, head and tail are two simple events. These two simple events make up the sample space. Further, the probability of an event occurring falls within the range of 0 to 1. The probability of an...
23.4K

You might also read

Related Articles

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

Sort by
Same author

Quantifying the Peripheral Surface Information Entropy from Conformational Ensembles of Globular Protein-Peptide Complexes.

Biophysical journal·2026
Same author

Small Intestinal Bacterial Overgrowth (SIBO) - Prevention and Therapeutic Role of Nutrition, Prebiotics, Probiotics, and Prokinetics.

Current pharmaceutical design·2025
Same author

Climate Effects on Belowground Tea Litter Decomposition Depend on Ecosystem and Organic Matter Types in Global Wetlands.

Environmental science & technology·2024
Same author

<i>Ab initio</i> gene prediction for protein-coding regions.

Bioinformatics advances·2023
Same author

Improving Compliance of Physicians in Reporting and Documenting Critical Alerts in a Cancer Hospital.

Journal of cancer & allied specialties·2023
Same author

Variation in carbon and nitrogen concentrations among peatland categories at the global scale.

PloS one·2022
Same journal

Research on a Regional Availability Evaluation Model for Road-Area High-Entropy Energy Based on Synergy Factors.

Entropy (Basel, Switzerland)·2026
Same journal

Atmospheric Turbulence Channel Modeling and Performance Analysis of a CO-ZP-OFDM Coherent Optical Communication System for UAV Air-to-Ground Scenarios.

Entropy (Basel, Switzerland)·2026
Same journal

Information Geometry and Asymptotic Theory for SMML Estimators.

Entropy (Basel, Switzerland)·2026
Same journal

Correlation Entropy and Power-Law Kinetics.

Entropy (Basel, Switzerland)·2026
Same journal

Research on the Contagion of Systemic Financial Risk Under the Impact of Climate Risks-From the Perspective of Complex Networks and Machine Learning.

Entropy (Basel, Switzerland)·2026
Same journal

The Statistical-Mechanical Meaning of the Wave Function of Quantum Mechanics.

Entropy (Basel, Switzerland)·2026
See all related articles

Related Experiment Video

Updated: Feb 1, 2026

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

5.1K

Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories.

Jenny Farmer1, Fareeha Kanwal1, Nikita Nikulsin2

  • 1Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Entropy (Basel, Switzerland)
|December 1, 2018
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations reveal significant differences in protein dynamics between native and mutant proteins. New statistical methods, beyond root mean square fluctuation, offer more sensitive comparisons of protein conformational ensembles.

Keywords:
beta-lactamaseconformational fluctuationsconformational similarity measuresmolecular dynamicsp-valuessite directed mutationsstatistical significance

More Related Videos

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.3K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K

Related Experiment Videos

Last Updated: Feb 1, 2026

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

5.1K
Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation
15:05

Deciphering the Structural Effects of Activating EGFR Somatic Mutations with Molecular Dynamics Simulation

Published on: May 20, 2020

9.3K
Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid
08:54

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

Published on: January 25, 2020

6.0K

Area of Science:

  • Computational biology
  • Biophysics
  • Structural biology

Background:

  • Molecular dynamics (MD) simulations are crucial for studying protein dynamics.
  • Inferring functional differences from conformational ensembles is common in structure-function studies.
  • Root mean square fluctuation (RMSF) is a standard measure for dynamics, but may lack sensitivity.

Purpose of the Study:

  • To compare novel statistical measures for quantifying differences in protein dynamics from MD simulations.
  • To evaluate the effectiveness of these measures in detecting subtle conformational changes, especially in mutation studies.
  • To assess the statistical significance of observed dynamic differences.

Main Methods:

  • Employed six MD trajectories for three native/mutant beta-lactamase pairs.
  • Utilized Jensen-Shannon divergence, modified Kullback-Leibler divergence, and local p-values from Kolmogorov-Smirnov tests.
  • Estimated probability density functions using a nonparametric maximum entropy method for rare event quantification.
  • Applied measures to both on-residue (Cα atom fluctuations) and residue-residue (distance fluctuations) dynamics.

Main Results:

  • New statistical measures revealed significant differences in protein dynamics between native and mutant proteins.
  • The nonparametric maximum entropy method effectively quantified rare events in the probability density functions.
  • Statistically significant differences were consistently observed between pairs of 100 ns all-atom simulations for moderate-sized proteins.
  • Extraordinarily low p-values indicated high confidence in detected dynamic differences.

Conclusions:

  • Standard RMSF may underestimate dynamic differences between protein conformations.
  • Advanced statistical methods provide more sensitive and robust comparisons of protein dynamics from MD simulations.
  • These enhanced methods are valuable for structure-function relationship studies, particularly those involving mutations.