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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 Families02:47

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism.   Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members.   If these new proteins contain similar amino acids in key locations, 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...

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Related Experiment Video

Updated: Jun 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

PIPs: human protein-protein interaction prediction database.

Mark D McDowall1, Michelle S Scott, Geoffrey J Barton

  • 1School of Life Sciences Research, College of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.

Nucleic Acids Research
|November 8, 2008
PubMed
Summary
This summary is machine-generated.

The PIPs database offers novel human protein-protein interaction predictions, identifying over 34,000 new interactions. This resource aids in understanding complex biological networks.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Last Updated: Jun 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

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay (PCA) in Living Cells
08:38

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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:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Existing databases lack comprehensive coverage of human PPIs.
  • Predictive modeling can identify novel interactions.

Purpose of the Study:

  • To introduce the PIPs database, a novel resource for human protein-protein interactions.
  • To provide a comprehensive collection of predicted PPIs, including many not found in existing databases.
  • To facilitate the study and modeling of human protein interaction networks.

Main Methods:

  • Utilized a Bayesian method integrating multiple data sources: expression, orthology, domain co-occurrence, post-translational modifications, and sub-cellular location.
  • Incorporated network topology into interaction prediction algorithms.
  • Developed a web interface for browsing, searching, and visualizing predicted interactions.

Main Results:

  • The PIPs database contains predictions for over 37,000 high-probability human protein-protein interactions.
  • >34,000 of these predicted interactions are novel, not reported in HPRD, BIND, DIP, or OPHID.
  • Predictions are ranked by likelihood, with contributions from each data source detailed.

Conclusions:

  • The PIPs database represents a significant expansion of known human protein-protein interactions.
  • It offers a user-friendly platform for exploring and analyzing interaction networks.
  • PIPs is a valuable resource for systems biology research and interaction network modeling.