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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...
Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
Convergence and divergence, and cross-talk between signaling pathways
Two distinct signaling pathways can converge on a single functional unit, which may either be a single protein or a complex of proteins. The response is either functionally distinct or synergistic between the two pathways but different from the response...

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Related Experiment Video

Updated: May 9, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
11:19

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

Reconstruction of signaling network from protein interactions based on function annotations.

Wei Liu1, Dong Li, Yunping Zhu

  • 1Teaching and Research Office, Department of Automatic Control, College of Mechanical & Electronic Engineering and Automatization, National University of Defense Technology, Kaifu District, Changsha 410073, Hunan, China.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|August 10, 2013
PubMed
Summary

This study introduces a new method using protein functional annotations to predict the directionality of protein-protein interactions. This approach accurately constructs signaling networks, aiding in understanding life processes.

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Last Updated: May 9, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Molecular Biology

Background:

  • Protein interactions form complex signaling networks crucial for understanding life processes.
  • Inferring the directionality of these interactions is essential for network construction.

Purpose of the Study:

  • To develop a novel method for inferring directionality in protein-protein interaction networks.
  • To construct accurate signaling networks based on predicted interaction directionality.

Main Methods:

  • Proposed a novel parameter, Gene Ontology Direct Score (GODS), based on protein functional annotations.
  • Developed a prediction model utilizing the GODS parameter.
  • Validated the method using fivefold cross-validation.

Main Results:

  • Achieved high sensitivity and specificity in predicting protein interaction directionality.
  • Attained 95.56% accuracy and 74.69% coverage on a human test set with a GODS threshold of 2.
  • Successfully reconstructed known human signaling pathways.

Conclusions:

  • The GODS-based method offers an effective approach to unraveling unknown signaling pathways.
  • Provides deeper insights into signaling networks by analyzing protein function and interaction directionality.