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Related Concept Videos

Protein-protein Interfaces02:04

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...
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Protein Networks02:26

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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.
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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.
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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
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DAPPER: a data-mining resource for protein-protein interactions.

Syed Haider1, Zoltan Lipinszki2, Marcin R Przewloka2

  • 1Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD UK.

Biodata Mining
|September 26, 2015
PubMed
Summary
This summary is machine-generated.

DAPPER is a new database and tool for analyzing protein-protein interactions in Drosophila melanogaster. It integrates diverse datasets, offering insights into complex biological mechanisms.

Keywords:
Data-integrationDrosophila melanogasterMass spectrometryProtein complexesProtein-protein interactionsProteomics data mining

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Area of Science:

  • Proteomics
  • Systems Biology
  • Bioinformatics

Background:

  • Understanding protein-protein interactions is crucial for elucidating biological mechanisms.
  • Large-scale datasets, particularly from model organisms like Drosophila melanogaster, necessitate specialized data analysis tools.
  • Existing resources require seamless integration and analysis capabilities for protein interaction data.

Purpose of the Study:

  • To introduce DAPPER, a database and mining tool for protein-protein interactions in Drosophila melanogaster.
  • To provide a comprehensive resource for studying multi-protein complexes in this model organism.

Main Methods:

  • Protein-protein interaction data compiled from mass spectrometric analyses of affinity-purified protein complexes.
  • Web access via accelerated BioMart software for customized data mining and querying.
  • Integration with FlyBase and Ensembl databases using BioMart's data-federation model for multi-dataset queries.

Main Results:

  • DAPPER provides a proteomics database of protein-protein interactions in Drosophila melanogaster.
  • Web-based data mining is enabled through customized querying and output formats.
  • The dataset is annotated with FlyBase identifiers and linked to Ensembl, facilitating complex queries.

Conclusions:

  • DAPPER serves as an accessible and extensible platform for integrating diverse protein-protein interaction resources.
  • It enables real-time analysis of new and existing Drosophila melanogaster interaction datasets.
  • The open-source nature ensures free availability of contents and source code.