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 Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.9K
Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
2.9K
Protein Organization01:24

Protein Organization

10.2K
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....
10.2K
Protein Organization01:13

Protein Organization

25.2K
25.2K
Protein Organization01:13

Protein Organization

162.6K
Overview
162.6K
Protein Organization01:24

Protein Organization

10.1K
10.1K
Structural Protein Function01:56

Structural Protein Function

3.4K
3.4K

You might also read

Related Articles

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

Sort by
Same author

Prioritizing Stability-enhancing Mutations using the ESM Protein Language Model in conjunction with Physics-based MM/GBSA Predictions.

Protein engineering, design & selection : PEDS·2026
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

Related Experiment Video

Updated: Apr 19, 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

16.2K

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

Lars Skjærven1,2, Xin-Qiu Yao3, Guido Scarabelli4

  • 1Department of Biomedicine, University of Bergen, Bergen, Norway. lars.skjarven@biomed.uib.no.

BMC Bioinformatics
|December 11, 2014
PubMed
Summary

Bio3D now integrates protein sequence, structure, and simulation data for evolutionary analysis. This allows researchers to study protein dynamics across entire families, providing deeper mechanistic insights.

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

1.4K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.5K

Related Experiment Videos

Last Updated: Apr 19, 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

16.2K
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

1.4K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

21.5K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Structural Biology

Background:

  • Traditional bioinformatics methods for protein dynamics analysis (crystallography, molecular dynamics, normal mode analysis) are often analyzed separately.
  • Relating protein motion to sequence evolution and function across protein families is challenging due to a lack of integrated tools.

Purpose of the Study:

  • To integrate evolutionary sequence, structure, and simulation analysis into the Bio3D package.
  • To provide tools for analyzing protein dynamics across large protein families.

Main Methods:

  • High-throughput normal mode analysis for proteins with varying sequences and structures.
  • Quantification of dynamical couplings using correlation network analysis.
  • Integration with biomolecular databases and comparative structural analysis methods.
  • Comparison of normal modes, molecular dynamics, and principal component analysis results.

Main Results:

  • The updated Bio3D package offers integrated analysis of protein structure, dynamics, and evolution.
  • New methods enable high-throughput normal mode analysis and quantification of dynamical couplings.
  • Demonstrated capabilities with dihydrofolate reductase and G-protein families.

Conclusions:

  • The integrated Bio3D package facilitates the study of dynamical features across protein families.
  • Enables researchers to move beyond single protein dynamics to family-wide evolutionary dynamics.
  • Bio3D is available as a free, platform-independent R package with comprehensive documentation.