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STRUCLA: a WWW meta-server for protein structure comparison and evolutionary classification.

Joanna M Sasin1, Michal A Kurowski, Janusz M Bujnicki

  • 1Bioinformatics Laboratory, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.

Bioinformatics (Oxford, England)
|July 12, 2003
PubMed
Summary

We developed STRUCLA, a web tool for building protein evolutionary trees using 3D structure comparisons. This method complements sequence analysis, especially for distantly related proteins.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein evolution

Background:

  • Protein evolutionary relationships are traditionally inferred from sequence alignments.
  • Functional constraints on evolutionary divergence primarily impact tertiary protein structure.
  • While structural comparisons can build phylogenetic trees, accessible tools are lacking.

Purpose of the Study:

  • To develop a convenient, publicly available web tool for constructing phylogenetic trees based on protein structures.
  • To provide an alternative and complementary method to sequence-based phylogenetic analysis.

Main Methods:

  • Developed STRUCLA (STRUcture CLAssification), a WWW tool for phylogenetic tree generation.
  • Input: User-provided PDB files or aligned protein coordinates.

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  • Methods: Utilizes various distance measures and user-defined cutoffs for structural comparison.

    • Main Results:

    • Generates unrooted trees in NEXUS format and distance matrices.
    • Provides a consensus tree for comprehensive evolutionary insights.
    • Demonstrates utility in the 'twilight zone of homology' where sequence data is unreliable.

    Conclusions:

    • STRUCLA offers a valuable tool for protein structure-based phylogenetics.
    • The tool complements existing sequence-based methods, enhancing evolutionary analysis.
    • Enables robust phylogenetic inference for distantly related proteins based on structural data.