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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 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...
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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Updated: May 10, 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

Complementing the Eukaryotic Protein Interactome.

Robert Pesch1, Ralf Zimmer

  • 1Institute for Informatics, Ludwig-Maximilians-Universität München, Munich, Germany.

Plos One
|July 5, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a Random Forest method to accurately predict protein interactions across species. The approach significantly improves the reliability of transferred protein interaction data, enhancing biological network analysis.

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Published on: June 15, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein interaction networks are crucial for understanding biological processes, but data is limited to model organisms.
  • Transferring interaction data to other species is common but suffers from low confidence due to unclear transferability.
  • Existing filtering methods improve precision but drastically reduce the number of transferable interactions.

Purpose of the Study:

  • To develop a robust method for scoring transferred protein interactions with high confidence.
  • To improve the accuracy and reliability of protein interaction network inference in non-model organisms.

Main Methods:

  • Utilized a Random Forest model trained on a comprehensive set of features derived from source and target networks, and ortholog annotations.
  • Evaluated interaction transfer from various eukaryotic organisms to Saccharomyces cerevisiae (S. cerevisiae).
  • Compared the Random Forest approach against common filtering techniques and other competing methods.

Main Results:

  • The Random Forest approach achieved an average transfer consistency of 85% for S. cerevisiae, a significant improvement over direct transfer (24%).
  • Successfully transferred nearly 70% of correctly transferable interactions while maintaining high consistency.
  • Outperformed existing methods in transferring interactions to species lacking experimental data.
  • Extended interactomes for Bos taurus, Mus musculus, and Gallus gallus by over 40,000 interactions each.

Conclusions:

  • The proposed Random Forest method provides a reliable and efficient way to score and transfer protein interactions across species.
  • This approach significantly enhances the prediction of protein functions and the construction of comprehensive interactomes for diverse organisms.
  • Publicly available web interface allows access to predicted interaction networks for various species and precision levels.