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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.
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
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...
Newman Projections02:06

Newman Projections

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 conformers.

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Related Experiment Video

Updated: Jun 3, 2026

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

ePMV embeds molecular modeling into professional animation software environments.

Graham T Johnson1, Ludovic Autin, David S Goodsell

  • 1Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Structure (London, England : 1993)
|March 15, 2011
PubMed
Summary
This summary is machine-generated.

Scientists can now easily prepare complex molecular data for publication and outreach using the embedded Python Molecular Viewer (ePMV). This open-source tool integrates molecular modeling software into 3D animation applications, simplifying data visualization and computational experiments.

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Area of Science:

  • Computational biology
  • Scientific visualization
  • Bioinformatics

Background:

  • Increasing research complexity poses challenges for data preparation for publication, education, and outreach.
  • Scientists often struggle with integrating diverse computational algorithms into their experimental workflows.
  • Existing tools may lack user-friendliness for researchers from varied backgrounds.

Purpose of the Study:

  • To develop an accessible solution for preparing complex scientific data.
  • To bridge the gap between computational algorithms and scientific visualization.
  • To facilitate interdisciplinary research and communication in molecular and cellular biology.

Main Methods:

  • Development of an open-source plug-in named embedded Python Molecular Viewer (ePMV).
  • Integration of molecular modeling software directly within professional 3D animation applications (hosts).
  • Creation of a unified interface for accessing scientific algorithms and animation capabilities.

Main Results:

  • ePMV provides simultaneous access to molecular modeling and 3D animation tools.
  • Users can create professional-quality visuals and perform computational experiments with greater ease.
  • Facilitates the exchange of algorithms between different scientific disciplines.

Conclusions:

  • ePMV reduces barriers in data preparation and computational experimentation for scientists.
  • The tool enhances interdisciplinary collaboration and communication in cellular and molecular biology.
  • Provides a common platform for visualizing complex biological data at the intersection of multiple fields.