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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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
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 13, 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

Modeling protein interacting groups by quasi-bicliques: complexity, algorithm, and application.

Xiaowen Liu1, Jinyan Li, Lusheng Wang

  • 1Department of Computer Science, City University of Hong Kong and Department of Computer Science and Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA. liuxiaowencs@gmail.com

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|May 1, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces quasi-bicliques to identify protein-protein interaction (PPI) sites within noisy biological data. A novel heuristic algorithm demonstrates improved performance in finding conserved motifs, advancing PPI network analysis.

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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
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Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Related Experiment Videos

Last Updated: Jun 13, 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

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry
14:58

Identification of Protein Complexes in Escherichia coli using Sequential Peptide Affinity Purification in Combination with Tandem Mass Spectrometry

Published on: November 12, 2012

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Modeling PPIs involves identifying interacting protein groups and conserved motifs.
  • Biological data often contains noise and incompleteness, posing challenges for analysis.

Purpose of the Study:

  • To develop a robust method for identifying interacting protein group pairs in PPI networks, accounting for data noise and incompleteness.
  • To introduce and analyze the computational complexity of the maximum vertex quasi-biclique and maximum balanced quasi-biclique problems.
  • To propose and evaluate a heuristic algorithm for finding quasi-bicliques in PPI networks.

Main Methods:

  • Utilized quasi-bicliques to model interacting protein group pairs in PPI networks.
  • Investigated the NP-hardness of the maximum vertex quasi-biclique and maximum balanced quasi-biclique problems.
  • Developed and applied a greedy heuristic algorithm for quasi-biclique discovery.

Main Results:

  • Proved that the maximum vertex quasi-biclique and maximum balanced quasi-biclique problems are NP-hard, contrasting with related polynomial-time solvable problems.
  • The proposed heuristic algorithm outperformed a benchmark algorithm in identifying matched motifs (BLOCKS and PRINTS).
  • Case studies showed successful mapping of identified interacting motif pairs to known interacting domain pairs in iPfam.

Conclusions:

  • Quasi-bicliques offer a promising approach for robustly identifying protein interaction sites from noisy PPI data.
  • The developed heuristic algorithm provides an efficient method for discovering these quasi-bicliques.
  • Findings contribute to improved understanding and modeling of protein-protein interactions and their functional implications.