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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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The new protein topology graph library web server.

Tim Schäfer1, Andreas Scheck1, Daniel Bruneß1

  • 1Molecular Bioinformatics, Institute of Computer Science, Johann Wolfgang Goethe-University Frankfurt am Main, Robert-Mayer-Str. 11-15, 60325 Frankfurt am Main, Germany and.

Bioinformatics (Oxford, England)
|October 9, 2015
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Summary

The Protein Topology Graph Library (PTGL) web server has been updated, offering enhanced protein topology analysis. This extended version provides new features for visualizing protein ligand graphs and identifying structural motifs, improving usability for researchers.

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein topology is crucial for understanding protein function and interactions.
  • Super-secondary structure level analysis provides insights into protein folding and stability.
  • Existing tools for protein topology analysis have limitations in scope and usability.

Purpose of the Study:

  • To introduce an extended version of the Protein Topology Graph Library (PTGL) web server.
  • To enhance the description and visualization of protein topology at the super-secondary structure level.
  • To provide researchers with improved tools for analyzing protein structural motifs and ligand interactions.

Main Methods:

  • The Protein Topology Graph Library (PTGL) server utilizes VPLG software for computing protein ligand graphs.
  • The web server is implemented using PHP, JavaScript, PostgreSQL, and Apache.
  • The server is accessible via major web browsers and includes an application programming interface (API).

Main Results:

  • The extended PTGL server offers comprehensive protein topology descriptions at the super-secondary structure level.
  • New features include detailed information on ligand binding to secondary structure elements.
  • The server enables computation and visualization of protein ligand graphs and facilitates the search for protein structural motifs.

Conclusions:

  • The updated PTGL web server provides an advanced platform for protein topology analysis.
  • Enhanced usability and an API allow for automated data retrieval and analysis.
  • The tool aids in understanding protein structure-function relationships and identifying novel structural motifs.