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 Networks02:26

Protein Networks

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,...
Protein Networks02:26

Protein Networks

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,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

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 polypeptide...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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 to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

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 to...

You might also read

Related Articles

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

Sort by
Same author

The integration of network pharmacology and multiomics reveals the mechanism by which Malus hupehensis leaves inhibit acute liver injury.

BMC complementary medicine and therapies·2026
Same author

BMI1 activated by ZBTB17 stabilizes SMAD2 to promote chondrocyte anabolism and alleviate osteoarthritis.

Journal of advanced research·2026
Same author

17q12 deletion syndrome presenting with chronic pancreatitis: a case report.

Frontiers in medicine·2026
Same author

An Injectable Photothermal Responsive Liposome Hydrogel Co-Loaded with Bufalin, Apatinib, and IR820 for Inhibiting Postoperative Recurrence of Colon Cancer.

International journal of nanomedicine·2026
Same author

SeOMLR: one-step multi-view latent representation with self-weighted ensemble learning for multi-omics cancer subtyping.

Bioinformatics (Oxford, England)·2026
Same author

Optical control of vortex lattices and magnetostriction in a confined quantum ferrofluid.

Optics letters·2026

Related Experiment Video

Updated: May 19, 2026

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

Exploring overlapping functional units with various structure in protein interaction networks.

Xiao-Fei Zhang1, Dao-Qing Dai, Le Ou-Yang

  • 1Center for Computer Vision and Department of Mathematics, Sun Yat-Sen University, Guangzhou, China.

Plos One
|August 24, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces a new model to find overlapping and diverse functional units in protein-protein interaction networks, improving upon existing methods for identifying protein complexes and other biological structures.

More Related Videos

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Related Experiment Videos

Last Updated: May 19, 2026

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

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Mapping Dysfunctional Protein-Protein Interactions in Disease
09:39

Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Network Science

Background:

  • Identifying functional units in protein-protein interaction (PPI) networks is crucial for understanding cellular organization.
  • Existing algorithms often focus on cohesive protein complexes and struggle with overlapping units or non-cohesive structures.
  • This limits their ability to fully represent the complexity of biological reality.

Purpose of the Study:

  • To develop a novel computational model for exploring overlapping and diverse structural functional units within PPI networks.
  • To overcome limitations of existing methods that primarily identify non-overlapping, cohesive protein complexes.

Main Methods:

  • Development of a regularized sparse random graph model (RSRGM).
  • RSRGM utilizes two key parameters to define functional units based on connection patterns and protein membership degrees.
  • A regularizer is incorporated to ensure smoothness in parameter estimation.

Main Results:

  • RSRGM demonstrates superior performance in detecting both cohesive and overlapping protein complexes compared to existing algorithms.
  • The model successfully identifies significant biological functional units beyond traditional protein complexes.
  • Experimental validation was conducted on four Saccharomyces cerevisiae PPI networks.

Conclusions:

  • The RSRGM provides a more comprehensive approach to identifying functional units in PPI networks.
  • It effectively captures overlapping and non-cohesive structures, offering a more accurate representation of cellular organization.
  • This advancement aids in a deeper understanding of biological complexity through network analysis.