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Related Concept Videos

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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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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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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Published on: February 8, 2017

Pathway databases and tools for their exploitation: benefits, current limitations and challenges.

Anna Bauer-Mehren1, Laura I Furlong, Ferran Sanz

  • 1Research Unit on Biomedical Informatics (GRIB), IMIM-Hospital del Mar, Universitat Pompeu Fabra, Barcelona Biomedical Research Park, Dr Aiguader 88, Barcelona, Spain.

Molecular Systems Biology
|July 30, 2009
PubMed
Summary

Manual curation of cell signalling pathways is labor-intensive. This review explores whether current pathway knowledge repositories are ready for systems biology analysis and drug target identification.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Molecular Biology

Background:

  • Cell signalling pathways are crucial for cellular function and disease mechanisms.
  • Manual literature curation for pathway reconstruction is resource-intensive.
  • Existing databases and analysis methods offer potential for systems biology approaches.

Purpose of the Study:

  • To discuss the readiness of cell signalling pathway knowledge repositories for systems biology.
  • To identify challenges and opportunities in utilizing pathway data for dynamic analysis.
  • To explore the potential for automatic data retrieval and integration.

Main Methods:

  • Literature review of existing cell signalling pathway databases.
  • Analysis of methodologies for data access and network reconstruction.
  • Discussion of mathematical modelling techniques for pathway dynamics.

Main Results:

  • Significant efforts have been made in creating comprehensive pathway representations.
  • Databases and analytical tools are available, but integration challenges remain.
  • The potential for systems biology applications is high, but repositories require further development.

Conclusions:

  • Current knowledge repositories show promise for systems biology but are not fully optimized.
  • Further development is needed to fully leverage pathway data for disease mechanism elucidation and drug discovery.
  • Initiating a discussion on repository readiness is crucial for advancing the field.