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Related Concept Videos

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 Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...
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...

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Related Experiment Video

Updated: May 26, 2026

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

Published on: January 26, 2024

A binary matrix factorization algorithm for protein complex prediction.

Shikui Tu1, Runsheng Chen2, Lei Xu1

  • 1Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.

Proteome Science
|December 15, 2011
PubMed
Summary
This summary is machine-generated.

A new Bayesian Ying-Yang harmony learning algorithm (BYY-BMF) effectively identifies protein complexes in protein-protein interaction networks. This method automatically determines cluster numbers and avoids parameter tuning, outperforming existing algorithms in robustness and accuracy.

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Last Updated: May 26, 2026

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

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment
09:02

Split-BioID — Proteomic Analysis of Context-specific Protein Complexes in Their Native Cellular Environment

Published on: April 20, 2018

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying protein complexes is crucial for understanding biological systems.
  • High-throughput protein-protein interaction (PPI) data contain noise (false-positives/negatives), complicating complex identification.

Purpose of the Study:

  • To develop a novel algorithm for robust protein complex detection in PPI networks.
  • To overcome limitations of existing methods, such as parameter dependency and pre-defined cluster numbers.

Main Methods:

  • Proposed a Binary Matrix Factorization (BMF) algorithm utilizing Bayesian Ying-Yang (BYY) harmony learning.
  • Applied BYY-BMF to factorize the adjacency matrix of PPI networks for protein clustering.
  • Developed an algorithm that automatically determines the number of protein clusters.

Main Results:

  • BYY-BMF automatically determines cluster numbers, unlike most BMF algorithms requiring pre-specification.
  • Clustering results are independent of parameters or thresholds, contrasting with methods like Markov Cluster Algorithm (MCL).
  • BYY-BMF demonstrated superior robustness and balanced prediction accuracy compared to MCL and spectral analysis on synthetic and real PPI networks.

Conclusions:

  • BYY-BMF offers a robust and accurate approach for identifying protein complexes from noisy PPI data.
  • The algorithm's parameter-free nature and automatic cluster number determination enhance its utility in biological network analysis.