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SymD webserver: a platform for detecting internally symmetric protein structures.

Chin-Hsien Tai1, Rohit Paul2, K C Dukka

  • 1Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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|May 7, 2014
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Summary

SymD is a new webserver that detects internal protein structure symmetry. This tool helps analyze protein structure, function, and modeling by visualizing symmetry properties interactively.

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Area of Science:

  • Structural bioinformatics
  • Computational biology
  • Protein science

Background:

  • Proteins can exhibit internal pseudo-symmetry within a single chain, distinct from the symmetry of multimeric complexes.
  • Understanding internal protein symmetry is crucial for analyzing protein structure, function, and modeling.
  • Existing tools may not adequately address the detection and visualization of internal protein symmetry.

Purpose of the Study:

  • To develop and present SymD webserver, a novel tool for detecting internal symmetry in protein structures.
  • To provide researchers with an accessible platform for studying protein symmetry properties.
  • To facilitate the analysis of protein structure, function, and modeling through symmetry insights.

Main Methods:

  • Implementation of the SymD algorithm into a web-based interactive tool.
  • Utilizing the Galaxy platform for extensibility and robust performance.
  • Interactive graphical visualization of symmetry properties, symmetry axis, and sequence alignments.

Main Results:

  • SymD webserver successfully detects and visualizes internal protein symmetry.
  • The tool provides interactive display of symmetry properties and sequence alignments.
  • It enables users to upload structures or retrieve them from databases for analysis.

Conclusions:

  • SymD webserver is the first tool of its kind for studying protein internal symmetry.
  • The webserver offers an intuitive interface for exploring protein symmetry properties.
  • It serves as a valuable resource for structural bioinformatics and protein research.