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

Arun S. Konagurthu, Ramanan Subramanian, Lloyd Allison, David Abramson, Maria Garcia de la Banda, Peter J. Stuckey, Arthur Lesk

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages123-131
Number of pages9
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1958
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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