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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-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 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,...
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: Jun 22, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Domain-oriented edge-based alignment of protein interaction networks.

Xin Guo1, Alexander J Hartemink

  • 1Department of Computer Science, Duke University, Durham, NC 27708-0129, USA. xinguo@cs.duke.edu

Bioinformatics (Oxford, England)
|May 30, 2009
PubMed
Summary
This summary is machine-generated.

We introduce a novel direct-edge alignment method for comparing protein-protein interaction networks across species. This approach effectively identifies conserved functional modules by analyzing domain interactions, outperforming existing methods.

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Last Updated: Jun 22, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

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Published on: July 14, 2015

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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • High-throughput experiments generate vast protein-protein interaction (PPI) data.
  • Comparative analysis of PPI networks across species aids in detecting conserved functional modules.
  • Network alignment is crucial for cross-species PPI network comparison.

Purpose of the Study:

  • To develop a novel network alignment paradigm for cross-species PPI analysis.
  • To move beyond traditional node-then-edge alignment to a direct-edge approach.
  • To identify conserved protein complexes by comparing domain interaction conservation.

Main Methods:

  • Proposed a direct-edge-alignment paradigm, bypassing explicit homologous protein identification.
  • Inferred alignable PPIs by comparing conservation of constituent domain interactions.
  • Applied the method to yeast-fly and yeast-worm PPI networks.

Main Results:

  • The direct-edge alignment approach successfully detected conserved protein complexes.
  • Outperformed two recent network alignment methods across most performance metrics.
  • Demonstrated the efficacy of domain interaction conservation for inferring PPI alignment.

Conclusions:

  • The direct-edge alignment paradigm offers an effective alternative for cross-species network analysis.
  • Comparing domain interaction conservation is a viable strategy for identifying conserved PPIs.
  • This method advances the field of network alignment for biological discovery.