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 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

Inactivation of two SARS-CoV-2 virus surrogates by electron beam irradiation on large yellow croaker slices and their packaging surfaces.

Food control·2022
Same author

Diamond-Blackfan anaemia caused by a de novo initiation codon mutation resulting in a shorter isoform of GATA1.

Clinical genetics·2022
Same author

Pnpla5-knockout rats exhibit reduced expression levels of proteins involved in steroid metabolism and wound healing compared to wild-type rats.

BMC genomics·2022
Same author

Nucleosome-Omics: A Perspective on the Epigenetic Code and 3D Genome Landscape.

Genes·2022
Same author

Changes in the Mucosa-Associated Microbiome and Transcriptome across Gut Segments Are Associated with Obesity in a Metabolic Syndrome Porcine Model.

Microbiology spectrum·2022
Same author

Expression Patterns Divergence of Reciprocal F<sub>1</sub> Hybrids Between <i>Gossypium hirsutum</i> and <i>Gossypium barbadense</i> Reveals Overdominance Mediating Interspecific Biomass Heterosis.

Frontiers in plant science·2022

Related Experiment Video

Updated: Jun 6, 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

A method based on local density and random walks for complexes detection in protein interaction networks.

Liang Yu1, Lin Gao, Kui Li

  • 1School of Computer Science and Technology, Xidian University, Xi'an, P R China. lyu@xidian.edu.cn

Journal of Bioinformatics and Computational Biology
|December 15, 2010
PubMed
Summary

We developed a Local Density and Random Walks (LDRW) method to detect protein complexes in protein-protein interaction networks. This approach effectively identifies biologically significant protein complexes, including overlapping ones.

More Related Videos

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: Jun 6, 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

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:

  • Computational Biology
  • Bioinformatics
  • Network Science

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding cellular functions.
  • Identifying protein complexes within these networks is a fundamental challenge in systems biology.
  • Existing methods often struggle with weighted networks or identifying overlapping complexes.

Purpose of the Study:

  • To introduce a novel method for detecting core-attachment protein complexes in PPI networks.
  • To enhance the accuracy and biological relevance of protein complex identification.
  • To address limitations of existing methods in handling weighted networks and overlapping complexes.

Main Methods:

  • The Local Density and Random Walks (LDRW) method employs a two-stage approach.
  • Stage 1: Identifies protein-complex cores using local subnetwork density.
  • Stage 2: Utilizes random walks with restarts to find attachment proteins for each core.

Main Results:

  • The LDRW method demonstrated effectiveness on two yeast PPI networks.
  • Validated predicted complexes against MIPS and Gene Ontology databases, confirming high biological significance.
  • Outperformed existing methods in identifying a greater number of biologically significant protein complexes.

Conclusions:

  • The LDRW method provides a significant improvement for protein complex detection.
  • It accurately identifies biologically significant protein complexes, including those that overlap.
  • This method offers a robust tool for analyzing complex biological systems through PPI networks.