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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,...
Overview of Cell-Matrix Interactions01:24

Overview of Cell-Matrix Interactions

The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...
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: Jun 19, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

The Interactorium: visualising proteins, complexes and interaction networks in a virtual 3-D cell.

Yose Y Widjaja1, Chi Nam Ignatius Pang, Simone S Li

  • 1School of Computer Science and Engineering, University of New South Wales, NSW, Australia.

Proteomics
|October 3, 2009
PubMed
Summary

The Interactorium tool visualizes complex yeast protein networks, complexes, and structures within a Virtual Cell. It simplifies complex data using new algorithms, advancing molecular biology visualization for various organisms.

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Last Updated: Jun 19, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces
07:42

In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Published on: March 19, 2010

Imaging Protein-protein Interactions in vivo
11:15

Imaging Protein-protein Interactions in vivo

Published on: October 10, 2010

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Molecular Visualization

Background:

  • Understanding intricate protein interactions is crucial for deciphering cellular mechanisms.
  • Existing visualization tools often struggle with the complexity of large-scale biological networks.

Purpose of the Study:

  • To introduce the Interactorium, a novel tool for visualizing biological networks.
  • To provide a user-friendly platform for exploring protein interactions, complexes, and structures within a cellular context.

Main Methods:

  • Development of the Interactorium tool utilizing a Virtual Cell environment.
  • Implementation of new algorithms for reducing visualization complexity, including putative complex generation and protein 'twin' reduction.
  • Design of toolboxes and menus for real-time data manipulation and display control.

Main Results:

  • The Interactorium can seamlessly visualize complex networks up to 40,000 proteins or 6,000 multiprotein complexes.
  • New algorithms effectively reduce visualization complexity, enabling clearer data representation.
  • The tool supports multi-level viewing of cellular molecular biology.

Conclusions:

  • The Interactorium represents a significant advancement over existing visualization approaches.
  • It is highly effective for Saccharomyces cerevisiae and applicable to prokaryotes and higher eukaryotes, including humans.
  • The Interactorium is available for download, facilitating broader research use.