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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...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...
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 22, 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

Assessing and predicting protein interactions by combining manifold embedding with multiple information integration.

Ying-Ke Lei1, Zhu-Hong You, Zhen Ji

  • 1Tongji University, 1239 Siping Road, Shanghai, PR China.

BMC Bioinformatics
|May 19, 2012
PubMed
Summary

This study introduces a computational method to improve the accuracy of protein-protein interaction (PPI) data by identifying errors. The new technique enhances the reliability of protein interaction networks.

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Last Updated: May 22, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
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Published on: March 3, 2015

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Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular processes.
  • High-throughput techniques generate vast PPI data but suffer from inaccuracies (false positives/negatives).
  • Accurate PPI data is essential for understanding cellular function.

Purpose of the Study:

  • To develop a robust computational method for assessing PPI reliability.
  • To predict novel protein interactions accurately.
  • To address the challenge of errors in high-throughput PPI data.

Main Methods:

  • Developed a computational technique integrating manifold embedding and multiple information integration.
  • Applied the method to yeast protein interaction networks (densely-connected and sparse).
  • Validated the method's performance in assessing and predicting interactions.

Main Results:

  • The proposed method effectively assesses interaction reliability and predicts new interactions.
  • Top-ranked interactions identified by the method exhibit high functional and localization coherence.
  • Experimental validation on yeast PPI networks demonstrated the method's efficacy.

Conclusions:

  • The developed method outperforms existing approaches for assessing and predicting protein interactions.
  • The algorithm is versatile, performing well on both dense and sparse PPI networks.
  • This approach offers a promising solution for detecting false positives and negatives in PPI networks.