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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 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,...
Predicting Reaction Outcomes02:24

Predicting Reaction Outcomes

Kinetics describes the rate and path by which a reaction occurs. In contrast, thermodynamics deals with state functions and describes the properties, behavior, and components of a system. It is not concerned with the path taken by the process and cannot address the rate at which a reaction occurs. Although it does provide information about what can happen during a reaction process, it does not describe the detailed steps of what appears on an atomic or a molecular level. On the other hand,...
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: Jul 10, 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

Computational prediction of domain interactions.

Philipp Pagel, Normann Strack, Matthias Oesterheld

    Methods in Molecular Biology (Clifton, N.J.)
    |November 21, 2007
    PubMed
    Summary

    Predicting protein domain interactions is crucial due to limited data. This study explores computational methods like phylogenetic profiling and protein-protein interaction inference to identify these domain relationships.

    More Related Videos

    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

    Related Experiment Videos

    Last Updated: Jul 10, 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
    • Structural Biology

    Background:

    • Conserved protein domains are fundamental to protein function, mediating interactions and forming binding pockets.
    • Existing databases lack comprehensive data on domain-level interactions, hindering computational analysis.
    • Understanding domain relationships is key to deciphering protein function and biological networks.

    Purpose of the Study:

    • To address the scarcity of domain-interaction data by exploring computational prediction methods.
    • To identify and analyze interacting and functionally linked protein domain pairs.
    • To evaluate the effectiveness of different computational approaches for domain-interaction prediction.

    Main Methods:

    • Utilized available experimental data from iPfam.
    • Employed phylogenetic profiling on conserved protein domains.
    • Inferred domain interactions from protein-protein interaction datasets.

    Main Results:

    • Demonstrated the feasibility of computational prediction for domain-domain interactions.
    • Evaluated the predictive power of phylogenetic profiling and PPI inference methods.
    • Highlighted the importance of integrating multiple computational approaches for robust predictions.

    Conclusions:

    • Computational methods are vital for predicting domain-domain interactions where experimental data is scarce.
    • Phylogenetic profiling and PPI inference offer valuable insights into domain relationships.
    • Combining diverse prediction strategies enhances the accuracy and reliability of identified domain interactions.