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

Protein Organization01:24

Protein Organization

9.8K
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....
9.8K
Protein Organization01:13

Protein Organization

159.3K
Overview
159.3K
Protein and Protein Structure02:15

Protein and Protein Structure

90.0K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
90.0K
Protein Folding01:22

Protein Folding

128.8K
Overview
128.8K
Protein Folding01:25

Protein Folding

11.9K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
11.9K
Protein Networks02:26

Protein Networks

4.6K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.6K

You might also read

Related Articles

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

Sort by
Same author

Contrasting Effects of Tagging Turnip Mosaic Virus Proteins.

Pathogens (Basel, Switzerland)·2026
Same author

Alanine Rewires the Communication Pathways Established During the Allosteric Activation of Liver Pyruvate Kinase by Fructose Bisphosphate.

Journal of chemical information and modeling·2026
Same author

Subsets of adjacent nodes (SOAN): A fast method for computing suboptimal paths in protein dynamic networks.

Molecular physics·2026
Same author

Effect of phosphorylation barcodes on arrestin binding to a chemokine receptor.

Nature·2025
Same author

Uncovering the Role of Distal Regions in PDK1 Allosteric Activation.

ACS bio & med chem Au·2025
Same author

Dissecting the Allosteric Fine-Tuning of Enzyme Catalysis.

JACS Au·2024

Related Experiment Video

Updated: Feb 25, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.1K

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web.

Shashank Jariwala1, Lars Skjærven2, Xin-Qiu Yao1

  • 1Department of Computational Medicine and Bioinformatics, University of Michigan Medical School.

Journal of Visualized Experiments : Jove
|July 27, 2017
PubMed
Summary

Bio3D-web offers an integrated online platform for analyzing biomolecular structures. It facilitates interactive exploration of protein sequence-structure-dynamic relationships for families and superfamilies.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K

Related Experiment Videos

Last Updated: Feb 25, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

16.1K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

1.2K
Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.6K

Area of Science:

  • Biochemistry and Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Analyzing biomolecular structures is crucial for understanding protein function and evolution.
  • Existing tools often require significant computational expertise and lack integrated workflows.
  • Investigating sequence-structure-dynamic relationships is complex and requires diverse analytical approaches.

Purpose of the Study:

  • To introduce and demonstrate Bio3D-web, an online application for interactive biomolecular structure analysis.
  • To provide a comprehensive workflow for exploring relationships between protein sequence, structure, and dynamics.
  • To enable researchers to easily investigate protein families and superfamilies.

Main Methods:

  • Utilizing Bio3D-web for interactive analysis of biomolecular structure data.
  • Implementing functionality for identifying similar protein structure sets based on user-defined thresholds.
  • Performing multiple sequence alignment and structure superposition.
  • Conducting sequence and structure conservation analysis.
  • Mapping inter-conformer relationships using principal component analysis (PCA).
  • Comparing predicted internal dynamics through ensemble normal mode analysis (NMA).

Main Results:

  • Bio3D-web successfully integrates multiple analytical functions into a single online platform.
  • The application allows for interactive identification of related protein structures.
  • It enables comprehensive analysis of sequence, structure, and dynamic properties.
  • The workflow supports the investigation of relationships within protein families and superfamilies.

Conclusions:

  • Bio3D-web provides a powerful and accessible online tool for biomolecular structure analysis.
  • The integrated functionality streamlines the investigation of sequence-structure-dynamic relationships.
  • This platform facilitates deeper insights into protein function, evolution, and dynamics.