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Recognizing complex, asymmetric functional sites in protein structures using a Bayesian scoring function.

Liping Wei1, Russ B Altman

  • 1Nexus Genomics, Inc., 229 Polaris Ave., Suite 6, Mountain View, CA 94043, USA. wei@nexusgenomics.com

Journal of Bioinformatics and Computational Biology
|August 4, 2004
PubMed
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This study introduces an improved FEATURE system for identifying functional sites in protein structures. The system accurately recognizes complex sites like ATP-binding and disulfide bonds without relying on conserved residues.

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The growing number of known 3D protein structures allows for statistical profiling of functional sites.
  • These profiles are crucial for automated annotation of novel protein structures.
  • Recognizing functional sites is key to understanding protein function and interactions.

Purpose of the Study:

  • To report an improved FEATURE system for recognizing functional sites in protein structures.
  • To demonstrate the system's ability to characterize complex and asymmetric sites.
  • To show FEATURE's utility in recognizing sites even without pre-existing statistical profiles.

Main Methods:

  • FEATURE defines multi-level physico-chemical properties of potential functional sites.

Related Experiment Videos

  • It analyzes the spatial distribution of these properties within the site's microenvironment.
  • A Bayesian scoring function compares query regions against statistical profiles of known sites and non-sites.

    • Main Results:

    • The improved FEATURE system accurately recognizes geometrically complex and asymmetric sites, including ATP-binding and disulfide bond-forming sites.
    • FEATURE's performance is independent of conserved residues or their geometry.
    • The system successfully identified redoxin active sites using an artificially constructed profile when no statistical profile was available.

    Conclusions:

    • The enhanced FEATURE system provides a robust method for identifying diverse functional sites in protein structures.
    • Its ability to use both data-driven and knowledge-based profiles broadens its applicability in structural annotation.
    • FEATURE offers a valuable tool for large-scale analysis of protein function and structural biology research.