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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,...
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...
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 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...

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Related Experiment Video

Updated: May 28, 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

DomPep--a general method for predicting modular domain-mediated protein-protein interactions.

Lei Li1, Bing Zhao, Jun Du

  • 1Department of Biochemistry, Siebens-Drake Medical Research Institute, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada.

Plos One
|October 18, 2011
PubMed
Summary
This summary is machine-generated.

DomPep predicts protein-protein interactions (PPIs) mediated by modular domains using proteomic data and sequence information. This method achieves high accuracy and coverage, outperforming existing tools for diverse domain families.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Last Updated: May 28, 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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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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

Area of Science:

  • Biochemistry
  • Computational Biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Modular domains binding to short linear motifs mediate many PPIs.
  • Existing prediction tools are often limited to specific domain types.

Purpose of the Study:

  • To develop a versatile computational method, DomPep, for predicting PPIs mediated by any modular domain.
  • To improve the accuracy and coverage of PPI prediction compared to existing approaches.
  • To enable PPI prediction for domains with and without experimental binding data.

Main Methods:

  • DomPep integrates proteomic binding data with protein sequence information.
  • It introduces a novel 'Ligand-Binding Similarity' parameter to calibrate prediction models.
  • Prediction models utilize Domain Sequence Identity and Position-Weighted-Matrix distance.

Main Results:

  • DomPep demonstrated superior accuracy and coverage in predicting PPIs for PDZ and SH2 domain families.
  • The method successfully predicted novel PPIs for human PDZ domains, validated by experimental assays.
  • Predictions were validated at the proteome scale, confirming DomPep's accuracy.

Conclusions:

  • DomPep offers a highly accurate and broadly applicable method for predicting modular domain-mediated PPIs.
  • Its reliance on sequence data allows for easy expansion to new domain types.
  • DomPep serves as a valuable discovery tool for identifying novel protein interactions.