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SURF'S UP! - protein classification by surface comparisons.

Joanna M Sasin1, Adam Godzik, Janusz M Bujnicki

  • 1Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland. asia@genesilico.pl

Journal of Biosciences
|April 12, 2007
PubMed
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SURF'S UP! is a new web server that compares protein surfaces to predict function. It quantifies similarities in physicochemical features, aiding in the functional characterization of hypothetical proteins.

Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Large-scale genomics projects yield many hypothetical proteins lacking functional annotation.
  • Existing homology-based methods for functional prediction are limited by tools for quantitative comparison of divergent residues.

Purpose of the Study:

  • To introduce SURF'S UP!, a web server for analyzing functional relationships in protein families.
  • To enable quantitative comparison of protein surface physicochemical features for functional inference.

Main Methods:

  • The SURF'S UP! server compares protein surface maps using an algorithm that scores physicochemical feature similarity (charge, hydrophobicity).
  • It utilizes protein coordinates as input and outputs spherical coordinates, similarity matrices, and neighbor-joining trees for clustering.

Related Experiment Videos

  • The method focuses on coarse surface features, allowing analysis of comparative models and non-homologous proteins with user-provided structural superposition.

    • Main Results:

    • SURF'S UP! assigns numerical similarity scores to protein surfaces based on physicochemical patterns.
    • It facilitates the recognition of protein clusters with similar surfaces and presumed similar functions.
    • The server provides graphical and matrix-based outputs for comparative analysis and phylogenetic tree construction.

    Conclusions:

    • SURF'S UP! offers a novel approach to infer protein function by comparing surface physicochemical features.
    • The tool aids in the functional characterization of hypothetical and homologous proteins.
    • Its ability to analyze coarse surface features and accommodate comparative models enhances its utility in structural genomics.