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Related Concept Videos

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,...
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...

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Related Experiment Video

Updated: May 14, 2026

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

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

Published on: March 3, 2015

Interactome3D: adding structural details to protein networks.

Roberto Mosca1, Arnaud Céol, Patrick Aloy

  • 1Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine, Barcelona, Spain.

Nature Methods
|February 13, 2013
PubMed
Summary
This summary is machine-generated.

Interactome3D provides atomic-resolution structural models for over 12,000 protein-protein interactions, aiding biological network analysis. This computational resource enables automated 3D modeling of newly discovered interactions and pathways.

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Related Experiment Videos

Last Updated: May 14, 2026

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08:38

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Published on: March 3, 2015

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Area of Science:

  • Systems Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Network-centered approaches are vital for understanding biological systems.
  • Limited molecular detail and experimental challenges hinder protein complex structure determination.
  • Computational modeling is crucial for elucidating protein-protein interactions.

Purpose of the Study:

  • To present Interactome3D, a novel resource for structural annotation and modeling of protein-protein interactions.
  • To provide atomic-resolution structural insights into biological networks.
  • To enable automated 3D modeling of user-submitted interactions and pathways.

Main Methods:

  • Integration of protein interaction data from major pathway repositories.
  • Development of automated pipelines for 3D model generation using structural templates.
  • Application of computational modeling for structural annotation of biological pathways.

Main Results:

  • Interactome3D offers structural details for over 12,000 protein-protein interactions across eight model organisms.
  • The resource supports the modeling of newly discovered interactions and pathways in any species.
  • Structural annotation of the complement cascade pathway revealed potential common mechanisms for disease mutations.

Conclusions:

  • Interactome3D enhances the understanding of molecular mechanisms within biological networks.
  • The platform facilitates the structural exploration of protein interactions, aiding biological research.
  • This resource provides valuable insights into disease-related mutations through structural analysis.