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 Shapes01:18

Molecular Shapes

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.
Two regions of electron density in a diatomic...
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.
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
Molecular Orbital Theory I02:35

Molecular Orbital Theory I

Overview of Molecular Orbital Theory
VSEPR Theory02:37

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:

You might also read

Related Articles

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

Sort by
Same author

PDBe-SIFTS: an open-source tool for Structure Integration with Function, Taxonomy, and Sequences, featuring improved alignment, scoring scheme, and accelerated search.

bioRxiv : the preprint server for biology·2026
Same author

The NMR Exchange Format (NEF): Specification and Applications.

bioRxiv : the preprint server for biology·2026
Same author

Generating 3D models of complex carbohydrates with GLYCAM-Web.

Nature methods·2026
Same author

MolViewStories: Interactive molecular storytelling.

Protein science : a publication of the Protein Society·2026
Same author

Mol* web molecular graphics engine.

Protein science : a publication of the Protein Society·2026
Same author

OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: May 7, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.7K

MolViewSpec: a Mol* extension for describing and sharing molecular visualizations.

Adam Midlik1, Sebastian Bittrich2, Jennifer R Fleming1

  • 1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge CB10 1SD, United Kingdom.

Nucleic Acids Research
|May 6, 2025
PubMed
Summary

MolViewSpec offers a standardized method for defining molecular visualizations, improving web accessibility and usability. This open standard enhances data interoperability and reproducibility in structural biology.

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.5K
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

756

Related Experiment Videos

Last Updated: May 7, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
10:52

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics

Published on: April 12, 2019

12.7K
Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

9.5K
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

756

Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Molecular visualization is crucial for structural biologists.
  • Current tools like Mol* Viewer have limitations in accessibility and usability.
  • A need exists for standardized, interoperable web-based molecular visualization.

Purpose of the Study:

  • Introduce MolViewSpec, a standardized approach to define molecular visualizations.
  • Enhance accessibility and usability of web-based molecular visualization.
  • Promote interoperability across different programming languages and viewers.

Main Methods:

  • Developed MolViewSpec as an open standard for scene definition.
  • Decoupled scene definition from rendering for flexibility.
  • Integrated support for structural, volumetric, and annotation data formats.
  • Created a Mol* extension and a standalone Python package.

Main Results:

  • MolViewSpec enables standardized definition of complex molecular scenes.
  • Supports visualization of diverse data formats with custom annotations.
  • Achieved broader interoperability and support across platforms.
  • Facilitates streamlined, reproducible visual molecular analyses.

Conclusions:

  • MolViewSpec enhances accessibility and usability of web-based molecular visualization.
  • The open standard promotes interoperability and reproducibility in structural biology.
  • MolViewSpec is available as a Mol* extension and Python package.