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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Structure description and identification using the tableau representation of protein folding patterns.

Arun S Konagurthu1, Arthur M Lesk

  • 1Clayton School of Information Technology, Monash University, Clayton, VIC, Australia. arun.konagurthu@monash.edu

Methods in Molecular Biology (Clifton, N.J.)
|September 19, 2012
PubMed
Summary

We created a protein folding pattern representation using secondary structure elements. This method helps analyze protein architecture and identify structural similarities.

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Area of Science:

  • Structural biology
  • Bioinformatics

Background:

  • Protein folding patterns are complex and crucial for function.
  • Understanding protein architecture requires analyzing secondary structure arrangements.

Purpose of the Study:

  • To present a novel tableau representation for protein folding patterns.
  • To enable mining of protein data bank for architectural studies.
  • To investigate relationships between local and global protein structures.

Main Methods:

  • Developed a concise tableau representation based on secondary structure order and contacts.
  • Utilized the protein data bank for database creation.
  • Applied methods to identify structural and substructural similarities.

Main Results:

  • A database of protein folding patterns represented by tableaux has been established.
  • The tableaux facilitate the study of general principles of protein architecture.
  • Methods for identifying structural similarities using tableaux are outlined.

Conclusions:

  • The tableau representation offers a powerful tool for analyzing protein folding patterns.
  • This approach aids in understanding protein architecture and structure-based relationships.
  • The developed methods enhance the identification of structural similarities in proteins.