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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...

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Related Experiment Video

Updated: May 14, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

XLink-DB: database and software tools for storing and visualizing protein interaction topology data.

Chunxiang Zheng1, Chad R Weisbrod, Juan D Chavez

  • 1Department of Chemistry, University of Washington , Seattle, Washington, United States.

Journal of Proteome Research
|February 19, 2013
PubMed
Summary

XLink-DB is a new tool for analyzing large-scale cross-linking data. It stores, visualizes, and analyzes protein interactions, replacing manual methods.

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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
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Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Related Experiment Videos

Last Updated: May 14, 2026

Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies
10:01

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Structural Biology

Background:

  • Manual analysis of large-scale cross-linking data is time-consuming and inefficient.
  • Developing automated tools is crucial for processing and visualizing complex protein interaction data.

Purpose of the Study:

  • To introduce XLink-DB, a novel software tool for the storage and visualization of cross-linking results.
  • To provide an automated platform for analyzing protein-protein interactions derived from cross-linking experiments.

Main Methods:

  • XLink-DB utilizes a relational database to store cross-linking data from various cross-linkers.
  • It automatically maps cross-linked sites onto Protein Data Bank (PDB) structures.
  • Protein interaction networks are generated, and results are compared with existing databases.

Main Results:

  • XLink-DB successfully stores and visualizes cross-linking data.
  • Automated mapping to PDB structures and comparison with existing databases are performed.
  • A comprehensive protein interaction network is generated from the entire dataset.

Conclusions:

  • XLink-DB offers an efficient solution for analyzing large-scale cross-linking data.
  • The tool facilitates the understanding of protein interactions and structural biology.
  • XLink-DB is available for non-commercial use with accessible source code.