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Protein structure similarity from Principle Component Correlation analysis.

Xiaobo Zhou1, James Chou, Stephen T C Wong

  • 1Center for Neurodegeneration and Repair, Center for Bioinformatics, Harvard Medical School, Boston, MA 02215, USA. zhou@crystal.harvard.edu

BMC Bioinformatics
|January 27, 2006
PubMed
Summary
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We introduce Principle Component Correlation (PCC) analysis to measure protein structural similarity beyond RMSD. This method effectively identifies homologous protein structures and topologies, even with different shapes.

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein structure databases are rapidly expanding, necessitating advanced comparison methods.
  • Current methods like RMSD are limited in detecting topological similarities in proteins with divergent shapes.
  • Understanding protein evolution and function relies on effective structure comparison.

Purpose of the Study:

  • To develop novel algorithms for extracting protein geometrical invariants.
  • To quantify both close and remote structural similarities.
  • To identify homologous protein structures and topologies.

Main Methods:

  • Constructing a symmetric interaction matrix using parameters between secondary structural elements.
  • Applying Principle Component Correlation (PCC) analysis to compare these matrices.

Related Experiment Videos

  • Utilizing distance and orientation as relationship parameters.

    • Main Results:

    • Strong correlations were observed between principle components of interaction matrices for structurally similar proteins.
    • PCC analysis successfully differentiated proteins with similar shapes but different topological arrangements.
    • Comparing maximum eigenvalues of independently defined matrices effectively clustered similar proteins.

    Conclusions:

    • PCC analysis is effective for comparing protein structures within the same topological class but differing in RMSD.
    • The method can distinguish proteins with similar shapes but varied topologies.
    • PCC analysis is flexible and adaptable to various structural parameters for protein comparison.