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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: Jun 18, 2026

Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
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Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling

Published on: November 17, 2019

STITCH 2: an interaction network database for small molecules and proteins.

Michael Kuhn1, Damian Szklarczyk, Andrea Franceschini

  • 1Biotechnology Center, TU Dresden, 01062 Dresden, Germany.

Nucleic Acids Research
|November 10, 2009
PubMed
Summary
This summary is machine-generated.

STITCH 2.0 integrates diverse data to map interactions between chemicals and proteins, expanding knowledge of drug-target relationships. This enhanced network aids large-scale analyses and links to chemical databases for broader research applications.

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Area of Science:

  • Bioinformatics
  • Cheminformatics
  • Systems Biology

Background:

  • Increasing volume of publicly available data on small molecule-protein interactions.
  • Need for integrated resources to navigate dispersed biological and chemical information.
  • Limitations of existing databases in providing comprehensive interaction networks.

Purpose of the Study:

  • To develop STITCH 2.0, an updated database integrating chemical-protein interactions.
  • To expand the network by incorporating data from BindingDB, PharmGKB, and the Comparative Toxicogenomics Database.
  • To provide a resource for interactive exploration and large-scale analysis of chemical-biological networks.

Main Methods:

  • Integration of data from literature, biological pathways, drug-target relationships, and binding affinity databases.
  • Inclusion of BindingDB, PharmGKB, and Comparative Toxicogenomics Database for enhanced interaction data.
  • Adoption of InChIKeys for standardized chemical identification and linking to external databases.

Main Results:

  • STITCH 2.0 connects proteins from 630 organisms with over 74,000 chemicals, including 2,200 drugs.
  • The database provides a comprehensive network of chemical-protein interactions.
  • Enhanced data integration and chemical identifiers facilitate broader usability.

Conclusions:

  • STITCH 2.0 represents a significant expansion of integrated chemical-protein interaction data.
  • The resource supports diverse research applications, from drug discovery to toxicogenomics.
  • Accessibility via http://stitch.embl.de/ enables broad scientific community use.