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

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.
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.
Fischer Projections02:18

Fischer Projections

Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines. While...
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...
Oriented Surfaces01:30

Oriented Surfaces

A surface is called orientable if a consistent choice of unit normal vector can be made at every point on the surface. A thin soap film stretched across a wire loop provides a familiar example. The film separates the air on one side from the air on the other, so one side can be selected as positive and the opposite side as negative. Once this choice is made, a unit normal vector can be assigned smoothly across the entire surface.At each point on the soap film, a unit normal vector points...
Distribution of Molecular Speeds01:27

Distribution of Molecular Speeds

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...

You might also read

Related Articles

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

Sort by
Same author

Lightweight dual-backbone network with attentional fusion for wound image classification.

Scientific reports·2026
Same author

Integrated image and location analysis for wound classification: a deep learning approach.

Scientific reports·2024
Same author

Multi-modal wound classification using wound image and location by deep neural network.

Scientific reports·2022
Same author

Multi-Barley Seed Detection Using iPhone Images and YOLOv5 Model.

Foods (Basel, Switzerland)·2022
Same author

Aberrant interhemispheric functional reciprocities of the default mode network and motor network in subcortical ischemic stroke patients with motor impairment: A longitudinal study.

Frontiers in neurology·2022
Same author

Ability of an altered functional coupling between resting-state networks to predict behavioral outcomes in subcortical ischemic stroke: A longitudinal study.

Frontiers in aging neuroscience·2022

Related Experiment Video

Updated: Jun 18, 2026

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

A list-based method for fast generation of molecular surfaces.

Zeyun Yu1

  • 1Department of Computer Science, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. yuz@uwm.edu

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
|December 8, 2009
PubMed
Summary

We developed a fast molecular surface generation method. This technique efficiently creates solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES) using a list-based sphere union approach.

More Related Videos

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Interactive Molecular Model Assembly with 3D Printing
06:15

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Related Experiment Videos

Last Updated: Jun 18, 2026

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies
07:31

Realistic Membrane Modeling Using Complex Lipid Mixtures in Simulation Studies

Published on: September 1, 2023

Interactive Molecular Model Assembly with 3D Printing
06:15

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Computer-aided drug design

Background:

  • Accurate molecular surface representation is crucial for understanding molecular interactions.
  • Existing methods for generating solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES) can be computationally intensive.
  • Efficient algorithms are needed for large-scale molecular simulations and analyses.

Purpose of the Study:

  • To present a novel, fast, and reliable method for generating molecular surfaces.
  • To focus on the efficient computation of solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES).
  • To provide a mesh-based representation suitable for further processing.

Main Methods:

  • A list-based method for representing and generating the union of multiple spheres with arbitrary radii.
  • Application of the method to compute solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES).
  • Representation of the generated surface using a quadrilateral mesh, with optional conversion to a triangular mesh.

Main Results:

  • Demonstration of a fast and reliable molecular surface generation process.
  • Efficient computation of solvent-accessible surfaces (SAS) and solvent-excluded surfaces (SES).
  • Generation of molecular surfaces represented by quadrilateral meshes, highlighting speed and quality.

Conclusions:

  • The proposed method offers a significant improvement in the speed and reliability of molecular surface generation.
  • The list-based sphere union approach provides an efficient way to compute SAS and SES.
  • The resulting quadrilateral mesh representation is versatile for various downstream computational tasks.