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Information-Theoretic Inference of an Optimal Dictionary of Protein Supersecondary Structures

  • Arun S. KonagurthuEmail author
  • Ramanan Subramanian
  • Lloyd Allison
  • David Abramson
  • Maria Garcia de la Banda
  • Peter J. Stuckey
  • Arthur M. Lesk
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1958)

Abstract

We recently developed an unsupervised Bayesian inference methodology to automatically infer a dictionary of protein supersecondary structures (Subramanian et al., IEEE data compression conference proceedings (DCC), 340–349, 2017). Specifically, this methodology uses the information-theoretic framework of minimum message length (MML) criterion for hypothesis selection (Wallace, Statistical and inductive inference by minimum message length, Springer Science & Business Media, New York, 2005). The best dictionary of supersecondary structures is the one that yields the most (lossless) compression on the source collection of folding patterns represented as tableaux (matrix representations that capture the essence of protein folding patterns (Lesk, J Mol Graph. 13:159–164, 1995). This book chapter outlines our MML methodology for inferring the supersecondary structure dictionary. The inferred dictionary is available at http://lcb.infotech.monash.edu.au/proteinConcepts/scop100/dictionary.html.

Key words

Minimum message length MML Tableau representation Protein folding pattern Supersecondary structure 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Arun S. Konagurthu
    • 1
    Email author
  • Ramanan Subramanian
    • 1
  • Lloyd Allison
    • 1
  • David Abramson
    • 2
  • Maria Garcia de la Banda
    • 1
  • Peter J. Stuckey
    • 1
    • 3
  • Arthur M. Lesk
    • 4
  1. 1.Faculty of Information TechnologyMonash UniversityClaytonAustralia
  2. 2.Research Computing CentreUniversity of QueenslandSt LuciaAustralia
  3. 3.Department of Computing and Information SystemsUniversity of MelbourneParkvilleAustralia
  4. 4.Department of Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkUSA

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