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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...
From DNA to Protein03:06

From DNA to Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...

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Related Experiment Video

Updated: May 24, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

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

Published on: January 26, 2024

Can simple codon pair usage predict protein-protein interaction?

Yuan Zhou1, Ying-Si Zhou, Fei He

  • 1State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

Molecular Biosystems
|March 7, 2012
PubMed
Summary
This summary is machine-generated.

Researchers discovered that codon pair usage differs between interacting proteins. This finding led to the development of CCPPI, a novel predictor for protein-protein interactions (PPIs) that outperforms existing sequence-based methods.

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

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

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Predicting PPIs is challenging, with sequence-based methods showing promise.
  • Homology-free encoding schemes are emerging for PPI prediction.

Purpose of the Study:

  • To investigate the relationship between codon pair usage and PPIs in yeast.
  • To develop a novel sequence-based predictor for PPIs using codon pair frequencies.
  • To evaluate the performance of the new predictor against existing methods.

Main Methods:

  • Analysis of codon pair usage in yeast protein interaction networks.
  • Development of a Support Vector Machine (SVM) predictor (CCPPI) using codon pair frequency differences.
  • 10-fold cross-validation on balanced and unbalanced yeast PPI datasets.

Main Results:

  • Interacting protein pairs exhibit significantly different codon pair usage compared to random expectations.
  • CCPPI demonstrated superior performance over other sequence-based encoding schemes on balanced datasets.
  • CCPPI achieved top performance on a large-scale unbalanced dataset.

Conclusions:

  • Codon pair usage provides valuable information for predicting PPIs, complementing amino acid-based methods.
  • Coordinated evolution of codon pairs in interacting proteins suggests functional linkage.
  • The CCPPI predictor offers an effective new approach for PPI identification.