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

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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.

You might also read

Related Articles

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

Sort by

Same author

OptimGS: a dual integrative genomic prediction framework for improving cold stress tolerance in wheat.

Briefings in bioinformatics·2026

Same author

Antioxidant potential and molecular diversity of passion fruit genotypes from Northeast India.

Scientific reports·2026

Same author

Genomic insights into end-use grain quality and nutritional traits of an ancient Indian dwarf wheat (Triticum sphaerococcum Percival) population using a multi-locus genome-wide association study.

Journal of the science of food and agriculture·2026

Same author

Targeting Biofilm Formation in Acinetobacter baumannii: In Silico Discovery of Novel Candidate Inhibitors for Acyl-Homoserine Lactone Synthase.

Current drug discovery technologies·2026

Same author

Promoting Microbiology Literacy and Holistic Health: IMiLI and IMiLI-SAC Perspectives on Microbes, Diet, Lifestyle and Society-A 5-Year Journey.

Microbial biotechnology·2026

Same author

Genome-wide association mapping and haplotype analysis reveal the genetic architecture of sodicity tolerance in bread wheat (Triticum aestivum L.).

Scientific reports·2026

Search research articles

Related Experiment Video

Updated: Oct 11, 2025

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Particle-Based Calculation and Visualization of Protein Cavities Using SES Models.

Li Feng, Feng Wang, Jian Zhang

IEEE Journal of Biomedical and Health Informatics

|November 29, 2021

Summary

This study introduces a new interactive method for visualizing and calculating molecular cavities in proteins, crucial for drug design. The approach clarifies cavity boundaries and allows user-guided selection for better drug discovery insights.

More Related Videos

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: Oct 11, 2025

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational biology
Structural bioinformatics
Drug discovery

Background:

Molecular cavities are critical for protein structure-based drug design.
Current cavity detection methods lack clear boundary definitions and interactive visualization.
Ambiguous cavity parameters hinder user understanding and interaction.

Purpose of the Study:

To develop a novel method for interactive cavity calculation and visualization.
To address the challenges of ambiguous cavity boundaries in computational drug design.
To enhance user-guided exploration of protein cavities.

Main Methods:

Combines two solvent-excluded surfaces (SES) models to define cavity boundaries.
Provides cavity emission points for better spatial understanding.
Implements a user-guided interactive system for cavity selection and tracking via clicking operations.
Utilizes position constraints for accurate cavity identification and filling.
Employs colorful depth perception for cavity representation.

Main Results:

The proposed method effectively identifies and calculates molecular cavities.
Interactive exploration and visualization of cavities are significantly improved.
User-guided selection enhances the usability of cavity analysis tools.
Accurate cavity boundary definition and tracking are achieved.

Conclusions:

The novel interactive method enhances the analysis of molecular cavities for drug design.
Improved cavity visualization and user interaction facilitate structure-based drug discovery.
This approach offers a more intuitive and effective way to explore protein binding sites.