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MAVL/StickWRLD: analyzing structural constraints using interpositional dependencies in biomolecular sequence

Hatice Gulcin Ozer1, William C Ray

  • 1Biophysics Graduate Program, The Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA.

Nucleic Acids Research
|July 18, 2006
PubMed
Summary
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The redesigned Multiple Alignment Variation Linker (MAVL) and StickWRLD tool now offers interactive Java applet visualizations for protein residue dependencies. This enhances molecular structure analysis and exploration of aggregate residue properties from pre-computed databases.

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Bioinformatics Tools

Background:

  • Structurally aligned protein families enable statistical methods to identify residue dependencies.
  • These dependencies have structural/functional implications and aid molecular structure refinement.
  • Previous MAVL/StickWRLD versions provided static VRML diagrams via web-form submission.

Purpose of the Study:

  • To report the complete redesign and rewrite of the MAVL/StickWRLD system.
  • To introduce a platform-independent Java applet with dynamic controls for intuitive data exploration.
  • To upgrade visualization capabilities for aggregate residue properties and provide access to pre-computed PFAM family diagrams.

Main Methods:

  • Development of a platform-independent Java applet for MAVL/StickWRLD.

Related Experiment Videos

  • Implementation of real-time dynamic controls for interactive data exploration.
  • Integration of visualization for aggregate residue properties and a database of pre-computed diagrams.

    • Main Results:

    • MAVL/StickWRLD is now a dynamic, interactive Java applet.
    • The system allows for more intuitive exploration and interaction with alignment data.
    • Visualization of aggregate residue properties and access to a PFAM family database are now available.

    Conclusions:

    • The redesigned MAVL/StickWRLD offers enhanced capabilities for analyzing protein residue dependencies.
    • The interactive Java applet facilitates a more intuitive understanding of molecular structures.
    • The tool provides valuable resources for structural bioinformatics research.