Related Experiment Video
Updated: Jun 30, 2026
12:53
Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
Published on: July 6, 2014
iRefIndex: a consolidated protein interaction database with provenance
Sabry Razick1, George Magklaras, Ian M Donaldson
1The Biotechnology Centre of Oslo, University of Oslo, PO Box 1125 Blindern, 0317 Oslo, Norway. sabry.razick@biotek.uio.no
BMC Bioinformatics
|October 1, 2008
Summary
A new method generates unique keys for protein interactions and participants, consolidating redundant data across multiple databases. This approach enhances protein interaction data retrieval and quality assessment.
Area of Science:
- Bioinformatics
- Computational Biology
- Proteomics
Background:
- Protein interaction data is fragmented across numerous databases.
- A unified approach is needed to efficiently search and manage this data.
- Redundant interaction records require systematic grouping and method documentation.
Purpose of the Study:
- To develop a method for creating a unifying index of protein interaction data.
- To group redundant interaction records and document the methods used for grouping.
- To facilitate searching and retrieval of protein interaction information.
Main Methods:
- Generate unique keys for protein interaction records and participant proteins using primary sequences, taxonomy identifiers, and Secure Hash Algorithm (SHA).
- Map protein database references to current protein sequence records, generating a mapping score to assess reference quality.
- Define redundant groups based on identical keys derived from identical protein sequences and taxonomy identifiers.
Main Results:
- A novel key generation method for protein interactions and participants.
- Identical keys indicate redundant interaction records referring to the same protein sequences and taxonomy identifiers.
- The mapping process provides feedback on problematic database references, improving data quality.
Conclusions:
- The developed method was applied to multiple protein interaction databases (BIND, BioGrid, DIP, HPRD, IntAct, MINT, MPact, MPPI, OPHID).
- A comprehensive protein interaction reference index in PSI-MITAB 2.5 format is available online.
- The index can support alternative redundant groupings based on gene identifiers or sequence identity.
Related Concept Videos
02:04Protein-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...
02:04Protein-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...
02:26Protein 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,...
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,...
02:26Protein 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,...
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,...
01:57Protein 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...
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...
01:57Protein 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...
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...