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Protein Networks

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 Interfaces

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 Parts

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 Parts

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...

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Related Experiment Video

Updated: Jun 30, 2026

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

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

Published on: April 1, 2017

Modifying the DPClus algorithm for identifying protein complexes based on new topological structures.

Min Li¹, Jian-er Chen, Jian-xin Wang

¹School of Information Science and Engineering, Central South University, Changsha, Hunan 410083, PR China. limin@mail.csu.edu.cn

BMC Bioinformatics

|September 26, 2008

Summary

A new algorithm, IPCA, identifies protein complexes in networks using a novel topological structure. IPCA effectively recalls known complexes and is robust to data errors, outperforming existing methods.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Protein complex identification is vital for understanding cellular organization and function.
Analyzing large protein-protein interaction datasets requires effective network-based algorithms to detect significant complexes.

Purpose of the Study:

To propose a novel topological structure for protein complexes.
To develop and present an algorithm, IPCA, for identifying protein complexes in large interaction networks based on this new structure.

Main Methods:

Developed a new topological structure combining subgraph diameter and density.
Proposed the IPCA clustering algorithm, expanding clusters from seeded vertices.
Applied IPCA to the Saccharomyces cerevisiae protein interaction network.

Main Results:

IPCA successfully identified numerous known protein complexes.
The algorithm demonstrated superior recall of known complexes compared to DPClus, CFinder, LCMA, MCODE, RNSC, and STM.
The proposed topological structure enables identification of dense subgraphs corresponding to protein complexes.

Conclusions:

The IPCA algorithm effectively identifies protein complexes using a new topological structure.
The method is robust against high rates of false positives and false negatives inherent in high-throughput interaction data.
The IPCA software is publicly available for research use.