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ViTO: tool for refinement of protein sequence-structure alignments.

Vincent Catherinot1, Gilles Labesse

  • 1Centre de Biochimie Structurale, INSERM U414, CNRS UMR5048, Université Montpellier 1 15, Avenue Charles Flahault 34060 Montpellier Cedex, France. catrino@cbs.cnrs.fr <catrino@cbs.cnrs.fr>

Bioinformatics (Oxford, England)
|July 24, 2004
PubMed
Summary

ViTO is a graphical application that integrates multiple sequence alignment editing and 3D structure viewing. This tool aids in refining sequence-structure alignments and characterizing protein families for comparative modeling.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Multiple sequence alignment (MSA) and 3D structure visualization are crucial in bioinformatics.
  • Handling complex biological structures and their corresponding alignments presents computational challenges.

Purpose of the Study:

  • To introduce ViTO, a graphical application for integrated multiple sequence alignment editing and 3D structure visualization.
  • To enable efficient manipulation and visualization of large alignments and complex structures.
  • To facilitate the refinement of sequence-structure alignments and characterization of protein families.

Main Methods:

  • ViTO provides an integrated graphical environment with an alignment editor and a 3D structure viewer.
  • The application supports 'multiparts' alignments for complex structures (multi-chain proteins, DNA, small molecules).

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  • ViTO connects alignment editing with 3D visualization for dynamic refinement and information mapping.

    • Main Results:

    • ViTO allows manipulation of hundreds of sequences and visualization of multiple structures simultaneously.
    • The linked editor and viewer enable rapid refinement of sequence-structure alignments by visualizing insertions/deletions in structural context.
    • Information on sequence conservation can be dynamically mapped onto 3D structures.

    Conclusions:

    • ViTO is a powerful tool for characterizing protein families.
    • The application optimizes alignments for comparative modeling by integrating sequence and structure information.
    • ViTO enhances the analysis of sequence-structure relationships in biological macromolecules.