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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 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 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,...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Related Experiment Video

Updated: May 20, 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

Protein complex prediction based on maximum matching with domain-domain interaction.

Wenji Ma1, Craig McAnulla, Lusheng Wang

  • 1Department of Computer Science, City University of Hong Kong, Hong Kong.

Biochimica Et Biophysica Acta
|July 10, 2012
PubMed
Summary

This study introduces a novel computational method for predicting protein complexes by integrating domain-domain interaction information. This approach significantly improves recall and precision, advancing protein interaction network analysis.

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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

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Last Updated: May 20, 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

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

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • High-throughput methods yield large protein-protein interaction networks.
  • Computational analysis is crucial for identifying functional modules like protein complexes.
  • Existing methods often neglect structural constraints in protein binding.

Purpose of the Study:

  • To develop a new computational method for protein complex prediction.
  • To incorporate domain-domain interaction information into network analysis.
  • To improve the accuracy and efficiency of protein complex detection.

Main Methods:

  • Formulated protein complex prediction as a maximum matching problem.
  • Integrated domain-domain interaction (DDI) prediction using Pfam, DOMINE, and InterDom databases.
  • Predicted DDIs by searching Pfam with hidden Markov models.
  • Compared performance against existing methods like Ozawa et al. (2010).
  • Combined the novel method with COACH, MCL, and MCODE.

Main Results:

  • The DDI prediction step significantly increased the number of edges in the DDI graph.
  • Recall value was at least doubled compared to the Ozawa et al. method.
  • Average precision showed a slight improvement.
  • Combining the method with COACH, MCL, and MCODE enhanced overall precision.

Conclusions:

  • The proposed method effectively leverages domain-domain interactions for improved protein complex prediction.
  • Integrating DDI information enhances the recall and precision of computational protein complex detection.
  • The approach offers a more robust and accurate way to analyze protein interaction networks.