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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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.

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Related Experiment Video

Updated: Jul 4, 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

Discovering functional interaction patterns in protein-protein interaction networks.

Mehmet E Turanalp1, Tolga Can

  • 1Department of Computer Engineering, Selcuk University, Alaaddin Keykubat Kampusu, 42075 Selcuklu, Konya, Turkey. eturanalp@selcuk.edu.tr

BMC Bioinformatics
|June 13, 2008
PubMed
Summary
This summary is machine-generated.

We developed PPISpan to find recurring functional patterns in protein-protein interaction networks. This method identifies novel interaction patterns beyond simple clusters or pathways, offering new insights into biological network organization.

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Last Updated: Jul 4, 2026

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

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Published on: March 3, 2015

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
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Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Network Biology

Background:

  • Analysis of biological networks, particularly protein-protein interaction (PPI) networks, is crucial for understanding cellular functions.
  • Existing research on PPI networks focuses on topology, evolution, conserved subnetworks, module discovery, and functional annotation.

Purpose of the Study:

  • To identify frequently occurring interaction patterns within the functional space of PPI networks.
  • To introduce a novel frequent pattern identification technique, PPISpan, tailored for PPI networks.

Main Methods:

  • Adapted PPISpan from the gSpan frequent subgraph identification method for PPI network analysis.
  • Mapped known protein functional annotations onto PPI networks.
  • Applied PPISpan to identify recurring functional interaction patterns in Saccharomyces cerevisiae PPI networks.

Main Results:

  • Identified a number of frequently occurring functional interaction patterns in Saccharomyces cerevisiae.
  • Demonstrated PPISpan's capability to find patterns in arbitrary topologies, differing from cluster or pathway-focused methods.

Conclusions:

  • PPISpan effectively identifies recurring functional interaction patterns in organismal PPI networks.
  • This approach provides a new perspective on the modular organization of biological networks.