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Related Experiment Videos

New opportunities for protease ligand-binding site comparisons using SitesBase.

N D Gold1, K Deville, R M Jackson

  • 1Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.

Biochemical Society Transactions
|May 22, 2007
PubMed
Summary
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SitesBase is a new database that maps protein ligand-binding sites. It helps researchers compare sites and discover new drug design and protein function relationships.

Area of Science:

  • Structural biology
  • Bioinformatics
  • Drug discovery

Background:

  • Growing structural data for protein ligand-binding sites is crucial for drug design.
  • Understanding ligand binding is key to predicting cross-reactivity and toxicity.

Purpose of the Study:

  • To develop SitesBase, a comprehensive database of protein ligand-binding sites.
  • To facilitate comparisons of binding sites and uncover structure-function relationships.

Main Methods:

  • Automated extraction of ligand-binding sites from the Macromolecular Structure Database.
  • Pre-calculation and storage of structural similarity data between binding sites.

Main Results:

  • SitesBase provides easy access to pre-calculated structural similarity information.

Related Experiment Videos

  • Enables binding-site comparisons for therapeutically relevant protein families (e.g., proteases).

    • Conclusions:

    • SitesBase supports structure-based drug design by providing valuable binding site data.
    • Facilitates the discovery of novel structure-function relationships for new proteins.