Related Experiment Video
Updated: May 24, 2026
08:38
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
Published on: March 3, 2015
Detecting overlapping protein complexes in protein-protein interaction networks.
Tamás Nepusz1, Haiyuan Yu, Alberto Paccanaro
1Department of Computer Science, Centre for Systems and Synthetic Biology, Royal Holloway, University of London, Egham Hill, Egham, UK.
Nature Methods
|March 20, 2012
Summary
We developed ClusterONE, a novel method for identifying overlapping protein complexes from protein-protein interaction data. ClusterONE accurately detects protein complexes and reveals their functional homogeneity.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- Protein-protein interactions (PPIs) are fundamental to cellular processes.
- Identifying protein complexes is crucial for understanding biological functions.
- Existing methods often struggle with overlapping complexes and accuracy.
Purpose of the Study:
- To introduce ClusterONE, a new algorithm for detecting overlapping protein complexes.
- To evaluate ClusterONE's performance against established methods using yeast PPI data.
- To assess the functional homogeneity of identified complexes.
Main Methods:
- Clustering with Overlapping Neighborhood Expansion (ClusterONE) algorithm.
- Utilized yeast protein-protein interaction datasets.
- Compared ClusterONE results with MIPS and SGD reference complexes.
- Evaluated performance against seven other popular complex detection methods.
Main Results:
- ClusterONE demonstrated superior performance in identifying known protein complexes compared to seven other methods.
- The method showed better correspondence with MIPS and SGD reference complexes.
- Identified protein complexes exhibited a high degree of functional homogeneity.
- Successfully detected potentially overlapping protein complexes.
Conclusions:
- ClusterONE is an effective and accurate method for detecting protein complexes, including overlapping ones.
- The algorithm provides a valuable tool for systems biology research.
- The functional homogeneity of ClusterONE-derived complexes supports their biological relevance.
Related Concept Videos
02:04Protein-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...
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
01:57Protein 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...
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...
01:57Protein 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...
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...