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

Irisin reverses insulin resistance in C2C12 cells via the p38-MAPK-PGC-1α pathway.

Peptides·2019
Same author

Role of Bile Acids in Dysbiosis and Treatment of Nonalcoholic Fatty Liver Disease.

Mediators of inflammation·2019
Same author

Circ_1639 induces cells inflammation responses by sponging miR-122 and regulating TNFRSF13C expression in alcoholic liver disease.

Toxicology letters·2019
Same author

Trisulfide-Bond Acenes for Organic Batteries.

Angewandte Chemie (International ed. in English)·2019
Same author

Annexin A1-mediated inhibition of inflammatory cytokines may facilitate the resolution of inflammation in acute radiation-induced lung injury.

Oncology letters·2019
Same author

Prenatal diagnosis of methylmalonic aciduria from amniotic fluid using genetic and biochemical approaches.

Prenatal diagnosis·2019

Related Experiment Video

Updated: May 26, 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

HKC: an algorithm to predict protein complexes in protein-protein interaction networks.

Xiaomin Wang1, Zhengzhi Wang, Jun Ye

  • 1Institute of Mechanical Engineering and Automation, National University of Defense Technology, Changsha 410073, China. wangxiaomin@nudt.edu.cn

Journal of Biomedicine & Biotechnology
|December 17, 2011
PubMed
Summary

A new algorithm, HKC, identifies protein complexes in large protein-protein interaction (PPI) networks. This method uses network topology to find dense clusters, improving complex prediction accuracy.

More Related Videos

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Related Experiment Videos

Last Updated: May 26, 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

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling
09:35

Resolving Affinity Purified Protein Complexes by Blue Native PAGE and Protein Correlation Profiling

Published on: April 1, 2017

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation
07:57

Quantification of Protein Interaction Network Dynamics using Multiplexed Co-Immunoprecipitation

Published on: August 21, 2019

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Genome-scale protein-protein interaction (PPI) networks are increasingly available.
  • Systematic analysis of large PPI datasets is a growing research area.
  • Identifying protein complexes within PPI networks is crucial for understanding cellular functions.

Purpose of the Study:

  • To present a novel topology-based algorithm, HKC, for detecting protein complexes in genome-scale PPI networks.
  • To improve the accuracy and efficiency of protein complex prediction methods.
  • To identify densely connected clusters within PPI networks that represent protein complexes.

Main Methods:

  • Developed a new algorithm named HKC (Highest k-core).
  • Utilized concepts of highest k-core and cohesion for complex prediction.
  • Focused on identifying overlapping clusters within PPI networks.
  • Employed a topology-based approach for network analysis.

Main Results:

  • The HKC algorithm successfully detected protein complexes in genome-scale PPI networks.
  • Experiments conducted on two datasets and two benchmarks demonstrated the algorithm's effectiveness.
  • HKC achieved a relatively high F-measure, indicating good prediction performance.
  • The algorithm showed improved performance compared to existing methods.

Conclusions:

  • HKC is an effective algorithm for predicting protein complexes in large PPI networks.
  • The method's reliance on network topology and overlapping cluster identification provides a robust approach.
  • HKC offers a valuable tool for systematic analysis of PPI data.
  • The findings suggest HKC can enhance our understanding of protein complex organization and function.