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Related Concept Videos

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 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 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...
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 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...

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

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

Published on: November 12, 2012

Which clustering algorithm is better for predicting protein complexes?

Charalampos N Moschopoulos1, Georgios A Pavlopoulos, Ernesto Iacucci

  • 1Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, 11527 Athens, Greece. mosxopul@ceid.upatras.gr.

BMC Research Notes
|December 22, 2011
PubMed
Summary
This summary is machine-generated.

This study evaluates clustering algorithms for identifying protein complexes from protein-protein interaction (PPI) data. MCL and RNSC algorithms show promise for predicting PPI complexes with high accuracy and quantity.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • Understanding PPI networks is crucial for deciphering molecular mechanisms.
  • High-throughput methods like yeast two hybrid and mass spectrometry are used to map PPIs.

Purpose of the Study:

  • To evaluate and compare the performance of four clustering algorithms for predicting protein complexes from PPI data.
  • To benchmark algorithm predictions against known protein complexes.
  • To assess the accuracy and efficiency of different clustering approaches in PPI network analysis.

Main Methods:

  • Four clustering algorithms (MCL, Spectral, RNSC, Affinity Propagation) were parameterized.
  • Algorithms were applied to six PPI datasets generated by Yeast 2 Hybrid (Y2H) and Tandem Affinity Purification (TAP).
  • Predicted protein complexes were compared and validated against existing databases.

Main Results:

  • MCL and RNSC algorithms demonstrated strong potential for predicting PPI complexes with high accuracy and in greater numbers.
  • Spectral clustering achieved the highest valid prediction rate but generated fewer valid clusters.
  • RNSC and MCL generally outperformed spectral clustering in geometrical accuracy.

Conclusions:

  • MCL and RNSC are promising algorithms for predicting protein complexes from PPI data.
  • Algorithm performance can vary with parameterization and dataset characteristics.
  • The study highlights metrics for evaluating the accuracy of PPI complex prediction.