An inductive logic programming approach to validate hexose binding biochemical knowledge

Houssam Nassif, Hassan Al-Ali, Sawsan Khuri, Walid Keirouz, David Page

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Scopus citations

Abstract

Hexoses are simple sugars that play a key role in many cellular pathways, and in the regulation of development and disease mechanisms. Current protein-sugar computational models are based, at least partially, on prior biochemical findings and knowledge. They incorporate different parts of these findings in predictive black-box models. We investigate the empirical support for biochemical findings by comparing Inductive Logic Programming (ILP) induced rules to actual biochemical results. We mine the Protein Data Bank for a representative data set of hexose binding sites, non-hexose binding sites and surface grooves. We build an ILP model of hexose-binding sites and evaluate our results against several baseline machine learning classifiers. Our method achieves an accuracy similar to that of other black-box classifiers while providing insight into the discriminating process. In addition, it confirms wet-lab findings and reveals a previously unreported Trp-Glu amino acids dependency.

Original languageEnglish (US)
Title of host publicationInductive Logic Programming - 19th International Conference, ILP 2009, Revised Papers
Pages149-165
Number of pages17
DOIs
StatePublished - Aug 3 2010
Externally publishedYes
Event19th International Conference on Inductive Logic Programming, ILP 2009 - Leuven, Belgium
Duration: Jul 2 2009Jul 4 2009

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5989 LNAI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other19th International Conference on Inductive Logic Programming, ILP 2009
CountryBelgium
CityLeuven
Period7/2/097/4/09

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Keywords

  • Aleph
  • ILP
  • binding site
  • hexose
  • protein-carbohydrate interaction
  • rule generation
  • substrate recognition

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Nassif, H., Al-Ali, H., Khuri, S., Keirouz, W., & Page, D. (2010). An inductive logic programming approach to validate hexose binding biochemical knowledge. In Inductive Logic Programming - 19th International Conference, ILP 2009, Revised Papers (pp. 149-165). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5989 LNAI). https://doi.org/10.1007/978-3-642-13840-9_14