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Related Experiment Videos

The proteome: structure, function and evolution.

Keiran Fleming1, Lawrence A Kelley, Suhail A Islam

  • 1Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK.

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|March 10, 2006
PubMed
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This study models protein sequence, structure, and function using a new tool, PHUNCTIONER. It accurately predicts protein function from structure, even with low sequence similarity.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Understanding protein sequence, structure, and function relationships is crucial in biology.
  • Current methods struggle with predicting function from structure when sequence similarity is low.

Purpose of the Study:

  • To develop and present computational methods for modeling protein sequence, structure, and function inter-relationships.
  • To create an automated pipeline for structural proteome annotation and a novel approach for function prediction.

Main Methods:

  • Developed an automated pipeline for structural annotation of proteomes, storing results in the 3D-GENOMICS database.
  • Created PHUNCTIONER, a method using Gene Ontology (GO) classification and structure-based sequence alignment to predict protein function.

Related Experiment Videos

  • Integrated 3D-GENOMICS with other databases for a comprehensive proteome annotation project (e-protein).

    • Main Results:

    • The 3D-GENOMICS database provides evolutionary insights through structural superfamily assignments.
    • PHUNCTIONER accurately predicts protein function from structure, outperforming closest structural homologue assignment in low sequence similarity regions (around 15%).
    • PHUNCTIONER can identify specific residues critical for protein family function.

    Conclusions:

    • The developed methods enhance our ability to model and predict protein function from structural data.
    • PHUNCTIONER offers a significant advancement in predicting protein function, particularly in challenging cases of low sequence homology.
    • The integrated database and prediction tools facilitate deeper understanding of proteomes and protein evolution.