Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Newman Projections

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...

Molecular Models

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.

Molecular Shapes

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...

Fischer Projections

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.

Gauss's Law: Planar Symmetry

Gauss's Law: Planar Symmetry

A planar symmetry of charge density is obtained when charges are uniformly spread over a large flat surface. In planar symmetry, all points in a plane parallel to the plane of charge are identical with respect to the charges. Suppose the plane of the charge distribution is the xy-plane, and the electric field at a space point P with coordinates (x, y, z) is to be determined. Since the charge density is the same at all (x, y) - coordinates in the z = 0 plane, by symmetry, the electric field at P...

Predicting Molecular Geometry

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries

You might also read

Related Articles

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

Sort by

Same author

Reaction-aware molecular representation learning: Toward generalizable artificial intelligence for enzymatic catalysis.

Acta pharmaceutica Sinica. B·2026

Same author

Molecular Topological Deep Learning for Polymer Property Prediction.

ACS nano·2026

Same author

The Hodge Laplacian advances inference of single-cell trajectories.

Nature methods·2025

Same author

Molecule Graph Networks with Many-Body Equivariant Interactions.

Journal of chemical theory and computation·2025

Same author

Topology-Enhanced Machine Learning Model (Top-ML) for Anticancer Peptide Prediction.

Journal of chemical information and modeling·2025

Same author

A cohomology-based Gromov-Hausdorff metric approach for quantifying molecular similarity.

Scientific reports·2025

Search research articles

Related Experiment Video

Updated: May 4, 2026

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Multiscale geometric modeling of macromolecules I: Cartesian representation.

Kelin Xia¹, Xin Feng, Zhan Chen

¹Department of Mathematics, Michigan State University, MI 48824, USA.

Journal of Computational Physics

|December 12, 2013

Summary

This study introduces novel variational multiscale surface models for biomolecular structures, resolving geometric singularities and minimizing free energy. The approach enhances data processing and enables new analyses for predicting protein binding sites.

Keywords:

Curvature analysis EMDataBank Free energy functional High order geometric PDEs Protein characterization Protein data bank Variational multiscale surfaces

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Related Experiment Videos

Last Updated: May 4, 2026

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Interactive Molecular Model Assembly with 3D Printing

Interactive Molecular Model Assembly with 3D Printing

Published on: August 13, 2020

Area of Science:

Computational biology
Biophysics
Geometric modeling

Background:

Biomolecular structures from Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB) present geometric singularities in their molecular surfaces (MS).
These singularities cause computational instabilities in simulations and violate surface free energy minimization principles.

Purpose of the Study:

To develop variational multiscale surface definitions and computational algorithms for biomolecular structures.
To address geometric singularities and improve the accuracy of molecular simulations.
To introduce novel methods for analyzing macromolecular surface morphology and predicting protein binding sites.

Main Methods:

Variational multiscale surface definitions based on geometric flows and solvation analysis.
Geometric and potential-driven Laplace-Beltrami flows for biomolecular surface evolution.
High-order partial differential equation (PDE)-based nonlinear filters for Electron Microscopy Data Bank (EMDB) data processing.
Application of diverse curvature definitions (Gaussian, mean, maximum, minimum, shape index, curvedness) and electrostatic surface potential analysis.
Introduction of 'polarized curvature' for binding site prediction.

Main Results:

Generated singularity-free biomolecular surfaces that minimize total free energy.
Demonstrated feature-preserving noise reduction in EMDB data using PDE-based filters.
Successfully applied novel curvature definitions and electrostatic potential analysis to macromolecular surfaces.
Introduced polarized curvature as a new concept for predicting protein binding sites.

Conclusions:

The proposed variational multiscale approach effectively resolves geometric singularities in biomolecular surfaces.
The developed methods enhance data processing, enable comprehensive surface analysis, and offer a new tool for predicting protein binding sites.