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Related Experiment Videos

Multiple Alignment of protein structures and sequences for VMD.

John Eargle1, Dan Wright, Zaida Luthey-Schulten

  • 1Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 607 South Mathews Avenue, Urbana, IL 61801, USA.

Bioinformatics (Oxford, England)
|December 13, 2005
PubMed
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Multiple Alignment is a new VMD plugin for analyzing protein structure alignments. It aids in visualizing similarities and performing evolutionary analyses, including phylogenetic tree construction.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Multiple protein structure alignment is crucial for understanding evolutionary relationships and functional similarities.
  • Existing tools may lack integrated features for both alignment analysis and evolutionary task execution.

Purpose of the Study:

  • Introduce Multiple Alignment, a novel VMD plugin for comprehensive protein structure alignment analysis.
  • Facilitate the visualization of sequence and structural similarity within aligned protein structures.
  • Enable advanced bioinformatic and evolutionary tasks, such as phylogenetic tree construction.

Main Methods:

  • Developed as a plugin for Visual Molecular Dynamics (VMD).
  • Integrates sequence and structure similarity visualization.

Related Experiment Videos

  • Supports the generation of structure-based phylogenetic trees and minimal basis sets.

    • Main Results:

    • Provides an intuitive interface for multiple protein structure alignments.
    • Enables detailed viewing of sequence and structural similarity levels.
    • Successfully implements evolutionary and bioinformatic analyses within VMD.

    Conclusions:

    • Multiple Alignment offers a powerful and integrated solution for protein structure alignment and analysis.
    • The plugin enhances the utility of VMD for structural bioinformatics research.
    • Facilitates deeper insights into protein evolution and function through structure-based analyses.