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

Predicting Molecular Geometry02:27

Predicting Molecular Geometry

35.6K
VSEPR Theory for Determination of Electron Pair Geometries
35.6K
Molecular Geometry and Dipole Moments02:36

Molecular Geometry and Dipole Moments

13.5K
The VSEPR theory can be used to determine the electron pair geometries and molecular structures as follows:
13.5K
Molecular Models02:00

Molecular Models

37.3K
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.
37.3K
Network Covalent Solids02:18

Network Covalent Solids

12.8K
Network covalent solids contain a three-dimensional network of covalently bonded atoms as found in the crystal structures of nonmetals like diamond, graphite, silicon, and some covalent compounds, such as silicon dioxide (sand) and silicon carbide (carborundum, the abrasive on sandpaper). Many minerals have networks of covalent bonds.
To break or to melt a covalent network solid, covalent bonds must be broken. Because covalent bonds are relatively strong, covalent network solids are typically...
12.8K
Molecular Comparison of Gases, Liquids, and Solids02:26

Molecular Comparison of Gases, Liquids, and Solids

50.0K
Particles in a solid are tightly packed together (fixed shape) and often arranged in a regular pattern; in a liquid, they are close together with no regular arrangement (no fixed shape); in a gas, they are far apart with no regular arrangement (no fixed shape). Particles in a solid vibrate about fixed positions (cannot flow) and do not generally move in relation to one another; in a liquid, they move past each other (can flow) but remain in essentially constant contact; in a gas, they move...
50.0K
Molecular Shapes01:18

Molecular Shapes

53.4K
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...
53.4K

You might also read

Related Articles

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

Sort by
Same author

Enhancing structural insights for advanced drug discovery by mitigating protein crystal damage.

Expert opinion on drug discovery·2025
Same author

Advances in cryo-electron microscopy (cryoEM) for structure-based drug discovery.

Expert opinion on drug discovery·2025
Same author

Metal ions in biomedically relevant macromolecular structures.

Frontiers in chemistry·2024
Same author

CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data.

IUCrJ·2024
Same author

Targeted removal of the FA2 site on human albumin prevents fatty acid-mediated inhibition of Zn<sup>2+</sup> binding.

Journal of lipid research·2024
Same author

The current role and evolution of X-ray crystallography in drug discovery and development.

Expert opinion on drug discovery·2023

Related Experiment Video

Updated: Apr 22, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

9.2K

DMG-α--a computational geometry library for multimolecular systems.

Robert Szczelina1, Krzysztof Murzyn

  • 1Faculty of Mathematics and Computer Science, ‡Malopolska Centre of Biotechnology, and §Faculty of Biochemistry, Biophysics and Biotechnology, Department of Computational Biophysics and Bioinformatics, Jagiellonian University , 31-007 Krakow, Poland.

Journal of Chemical Information and Modeling
|October 9, 2014
PubMed
Summary

Researchers can now perform detailed geometric analysis of molecular systems using the open-source DMG-α software. This computational biology tool offers advanced features for Voronoi diagrams, shape analysis, and solvent accessible surface area calculations.

More Related Videos

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

14.1K
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

2.0K

Related Experiment Videos

Last Updated: Apr 22, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
12:11

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry

Published on: April 8, 2020

9.2K
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

14.1K
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

2.0K

Area of Science:

  • Computational Biology
  • Molecular Chemistry
  • Biophysics

Background:

  • Geometric analysis of molecular systems is crucial in computational biology, chemistry, and biophysics.
  • Existing software may lack the necessary features or ease of use for fine-grained analysis.
  • There is a need for intuitive, high-performance tools for complex molecular geometry computations.

Purpose of the Study:

  • To introduce the DMG-α library, an open-sourced software for detailed geometric analysis of molecular systems.
  • To provide researchers with an intuitive and performant tool for various computational tasks.
  • To demonstrate the utility of DMG-α through sample analyses of biological molecules.

Main Methods:

  • Development of a C++ template-based library (DMG-α) for high performance.
  • Implementation of a Python interface (pydmga) for user convenience.
  • Computation of 3D power diagrams with periodic boundary conditions.
  • Calculation of approximate 2D Voronoi diagrams on arbitrary surfaces.
  • Shape properties recognition using α-shape theory.
  • Exact Solvent Accessible Surface Area (SASA) computation.

Main Results:

  • The DMG-α library provides robust capabilities for advanced geometric analysis.
  • Sample analyses successfully determined nontrivial geometric properties of *Escherichia coli*-specific lipids.
  • The software integrates molecular dynamics simulation data with geometric analysis.

Conclusions:

  • DMG-α offers a powerful and accessible solution for geometric analysis in computational biology, chemistry, and biophysics.
  • The library's features facilitate the discovery of complex molecular properties.
  • DMG-α enhances the study of molecular systems, particularly in the context of simulations and lipid analysis.