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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: Jul 7, 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

Protein function assignment through mining cross-species protein-protein interactions.

Xue-Wen Chen1, Mei Liu, Robert Ward

  • 1Bioinformatics and Computational Life-Sciences Laboratory, Information and Telecommunication Technology Center (ITTC), Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, Kansas, USA.

Plos One
|February 7, 2008
PubMed
Summary
This summary is machine-generated.

CSIDOP accurately predicts protein functions using protein-protein interaction data. This computational method assigns functions to uncharacterized proteins and enhances existing annotations.

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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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
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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

Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • The post-genome sequencing era faces challenges in assigning functions to uncharacterized proteins using high-throughput data.
  • Cross-species protein-protein interaction data offers a valuable resource for functional annotation.

Purpose of the Study:

  • To introduce CSIDOP, a novel computational method for protein function assignment.
  • To leverage shared interacting domain patterns from protein-protein interaction data for functional prediction.

Main Methods:

  • CSIDOP utilizes patterns of interacting protein domains across species.
  • The method was evaluated on the *H. sapiens* genome.

Main Results:

  • CSIDOP achieved 95.42% accuracy in predicting protein functions across 2,972 Gene Ontology (GO) categories.
  • Novel functional annotations were assigned to 181 previously uncharacterized proteins in *H. sapiens*.
  • CSIDOP identified potential additional functions for already characterized proteins, highlighting the complexity of protein roles.

Conclusions:

  • The CSIDOP method is demonstrated to be reliable and practical for protein function assignment.
  • The method's accuracy is expected to improve with increased availability of high-quality interaction data.
  • CSIDOP is scalable for genome-wide applications.