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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-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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell 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...
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...

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Related Experiment Video

Updated: May 9, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Identifying protein complexes from heterogeneous biological data.

Min Wu1, Zhipeng Xie, Xiaoli Li

  • 1School of Computer Engineering, Nanyang Technological University, Singapore.

Proteins
|July 16, 2013
PubMed
Summary

InteHC (Integrative Hierarchical Clustering) effectively identifies protein complexes by integrating diverse biological data. This method improves accuracy and outperforms 14 existing approaches for protein complex prediction.

Keywords:
data integrationhierarchical clusteringproteinprotein complexesprotein interactionsranking SVM

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Last Updated: May 9, 2026

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Published on: November 12, 2012

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Identification of protein complexes with quantitative proteomics in S. cerevisiae

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Systems Biology

Background:

  • Diverse biological data for proteins is increasingly available, necessitating data integration for tasks like function annotation and interaction prediction.
  • Integrating multiple data sources can improve protein interactome coverage but may introduce false positives, impacting protein complex prediction accuracy.

Purpose of the Study:

  • To present InteHC (Integrative Hierarchical Clustering), a novel method for identifying protein complexes from multiple data sources.
  • To address challenges of data integration, including false negatives and false positives, for accurate protein complex prediction.

Main Methods:

  • InteHC computes protein pair affinity scores from individual data sources.
  • A supervised model (linear ranking SVM) learns weights for combining source scores into a final matrix.
  • Hierarchical clustering is applied to the final score matrix to predict protein complexes.

Main Results:

  • Integration of heterogeneous data significantly benefits protein complex identification.
  • InteHC demonstrates superior performance compared to 14 state-of-the-art methods.
  • Experimental data and results are publicly available for download.

Conclusions:

  • InteHC provides an effective approach for accurate protein complex prediction by integrating heterogeneous biological data.
  • The method successfully mitigates issues associated with data integration, leading to improved performance.