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Protein-protein Interfaces

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 Interfaces

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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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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 Networks

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Updated: Jun 26, 2026

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions

A Data Integration Workflow to Identify Drug Combinations Targeting Synthetic Lethal Interactions

Published on: May 27, 2021

Interacting Species Database (ISDB): comprehensive resource for interspecies interactions at the molecular level.

Michael Mederer¹, Anupam Gautam^2,3, Oliver Kohlbacher^2,4,5

¹Department for Internal Medicine I (Gastroenterology, Hepatology, Endocrinology, and Metabolism), Medical University of Innsbruck, Innsbruck A-6020, Austria.

Bioinformatics (Oxford, England)

|June 25, 2026

Summary

The Interacting Species Database (ISDB) is a new resource cataloging molecular interactions between species. It provides valuable data for understanding ecological dynamics and interspecies relationships.

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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Ecology
Bioinformatics
Molecular Biology

Background:

Molecular interactions mediate crucial biological processes in ecological systems, including host-pathogen recognition and symbiosis.
Understanding these interspecies interactions at a molecular level is vital for mechanistic, evolutionary, and functional insights.
Current research is hindered by a lack of comprehensive molecular-level databases and limited experimental data.

Purpose of the Study:

To introduce a comprehensive resource for cataloging interspecies interactions at a molecular level.
To facilitate research on ecological dynamics by providing searchable and downloadable interaction data.
To enable researchers to deposit their own interspecies interaction data.

Main Methods:

Development of the Interacting Species Database (ISDB).
Annotation of interactions with NCBI taxonomic identifiers, interaction types, and molecular interaction details.
Creation of a web interface for data access and deposition.

Main Results:

The ISDB contains 858,229 interacting species pairs and 171,713 interspecies protein-protein interactions across 261,287 organisms.
The database is accessible via a web interface, with open-source code available on GitHub.
Data is archived on Zenodo for long-term accessibility.

Conclusions:

The ISDB significantly enhances the study of ecological dynamics by providing a centralized, molecular-level repository of interspecies interactions.
This resource supports diverse research domains by facilitating data sharing and analysis.
The ISDB promotes collaborative research and accelerates discoveries in interspecies molecular interactions.