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...
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, protein...

You might also read

Related Articles

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

Sort by
Same author

Soil fungal diversity and plant resilience under the dual stress of microplastics and heavy metals: A comparative study of lettuce and green onion.

Ecotoxicology (London, England)·2026
Same author

MetaCancerDB: a database of site-specific RNA-miRNA correlations in cancer metastasis.

Database : the journal of biological databases and curation·2026
Same author

Assessment of Macular Thickness in Myopic Patients and Its Correlation with Axial Length: A Hospital-Based Study.

Ophthalmic & physiological optics : the journal of the British College of Ophthalmic Opticians (Optometrists)·2026
Same author

A perturbed multilayer perceptron approach to predicting distant metastatic sites of cancer patients.

Computational biology and chemistry·2026
Same author

Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations.

Journal of bioinformatics and computational biology·2026
Same author

Uncertainty-Aware Learning of Multiple Conditions as a Framework for Streamlined Retention Time Prediction to Accelerate Method Development.

Analytical chemistry·2026
Same journal

Effects of CFR-PEEK plate layup and screw configuration on tibial shaft fracture healing: a simulation study based on a mechanobiological model.

Computer methods in biomechanics and biomedical engineering·2026
Same journal

Metabolic rate-limiting enzyme-associated genes as novel biomarkers for prognosis and treatment response in lung adenocarcinoma.

Computer methods in biomechanics and biomedical engineering·2026
Same journal

An interpretable, clinically-aligned AI paradigm for VTE risk prediction: an approach using LLMs and compound attention.

Computer methods in biomechanics and biomedical engineering·2026
Same journal

Effects of different resistance loads during resisted sprint running on internal stresses of the ankle joint: a finite element analysis.

Computer methods in biomechanics and biomedical engineering·2026
Same journal

Analysis of typical cases of medical infusion pump metering acceptance in nursing scenarios.

Computer methods in biomechanics and biomedical engineering·2026
Same journal

Investigation of biomechanical effect of inverted orthotic insoles on flexible flatfeet.

Computer methods in biomechanics and biomedical engineering·2026
See all related articles

Related Experiment Video

Updated: May 30, 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

ModuleSearch: finding functional modules in a protein-protein interaction network.

Guangyu Cui1, Rojan Shrestha, Kyungsook Han

  • 1School of Computer Science and Engineering, Inha University, Incheon, 402-751, South Korea.

Computer Methods in Biomechanics and Biomedical Engineering
|August 11, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces ModuleSearch, a tool for identifying functional modules in protein-protein interaction networks. It effectively finds protein groups with shared biological functions, aiding in predicting protein roles.

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

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Related Experiment Videos

Last Updated: May 30, 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

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Biological processes involve protein groups, not just individual proteins.
  • Proteins in the same biological process often form dense sub-graphs in protein-protein interaction networks.
  • Identifying these dense sub-graphs aids in predicting protein function and complexes.

Purpose of the Study:

  • To develop a heuristic algorithm for finding functional modules in protein-protein interaction networks.
  • To implement this algorithm in a standalone program called ModuleSearch.
  • To visualize identified protein modules.

Main Methods:

  • Developed a heuristic algorithm to detect dense sub-graphs representing functional modules.
  • Implemented the algorithm in the ModuleSearch program.
  • Applied ModuleSearch to a protein-protein interaction network of yeast proteins.

Main Results:

  • ModuleSearch identified 366 overlapping functional modules in the yeast interactome.
  • 71% of identified modules showed a shared function among over half their proteins.
  • 58% of modules had all proteins sharing a common function.
  • ModuleSearch outperformed other programs in finding more sub-graphs with a higher proportion corresponding to known functional modules.

Conclusions:

  • ModuleSearch is an effective tool for identifying functional modules in protein-protein interaction networks.
  • The identified modules provide valuable insights into protein functions and complexes.
  • ModuleSearch offers a robust method for biological network analysis and functional prediction.