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-protein Interfaces02:04

Protein-protein Interfaces

15.0K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
15.0K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.6K
4.6K
Protein Networks02:26

Protein Networks

4.7K
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,...
4.7K
Protein Networks02:26

Protein Networks

2.9K
2.9K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.2K
2.2K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
3.1K

You might also read

Related Articles

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

Sort by
Same author

Rafting kelp from California - is it alive? Physiological condition, ultrastructure and reaction to high UV treatment.

Protoplasma·2026
Same author

Seven deadly sins in artificial intelligence for digital medicine.

NPJ digital medicine·2026
Same author

Integrating AI into clinical practice: Human-centered design requirements for next-generation sequencing workflows.

Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society·2026
Same author

Implementing physics-informed neural networks with deep learning for differential equations.

Frontiers in artificial intelligence·2026
Same author

Applying traditional and machine learning-based GWAS approaches for marker-trait identification in wheat.

Frontiers in plant science·2026
Same author

From slides to AI-ready maps: Standardized multi-layer tissue maps as metadata for artificial intelligence in digital pathology.

Artificial intelligence in medicine·2026

Related Experiment Video

Updated: Apr 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K

Integrated web visualizations for protein-protein interaction databases.

Fleur Jeanquartier1, Claire Jean-Quartier2, Andreas Holzinger3,4

  • 1Research Unit HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, Graz, 8036, Austria. f.jeanquartier@hci-kdd.org.

BMC Bioinformatics
|June 17, 2015
PubMed
Summary
This summary is machine-generated.

This study surveys protein-protein interaction databases, recommending StringDB for visual analysis. It highlights the need for better visualization tools in bioinformatics for understanding complex biological networks.

More Related Videos

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
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

14.0K

Related Experiment Videos

Last Updated: Apr 10, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.8K
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
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

14.0K

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Understanding living systems requires knowledge of biological networks, particularly protein-protein interactions (PPIs).
  • Numerous bioinformatics databases and tools exist to aid in exploring PPIs for knowledge discovery and systems biology.
  • The diversity and volume of these resources can be overwhelming, hindering comprehensive understanding.

Purpose of the Study:

  • To survey and evaluate bioinformatics resources that enable the visual analysis of protein-protein interaction networks.
  • To identify the most effective tools for interactive visualization of PPI data.

Main Methods:

  • A systematic survey of 53 resources supporting network visualization was conducted.
  • Ten selected resources were evaluated based on interoperability, data integration, interaction quantity, visualization quality, and data coverage.
  • Comparative analysis was performed to assess usability and features.

Main Results:

  • Significant differences were found in usability, visualization capabilities, and data quantity among the evaluated resources.
  • StringDB emerged as the recommended resource for PPI network visualization.
  • CPDB offers a comprehensive dataset, while IntAct allows network layout customization.

Conclusions:

  • Only a subset of web resources with graph visualization effectively supports interactive visual analysis of PPIs.
  • Further enhancements in visualization integration within biochemical analysis tools are necessary.
  • Key challenges include improving data comprehensiveness, confidence scoring, interactive features, and overall visualization maturity.