title: An Inductive Logic Programming Approach to Validate Hexose Binding Biochemical Knowledge.
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.
authors.affiliation: Department of Computer Sciences, University of Wisconsin-Madison, USA.
authors.forename: Houssam
authors.initials: H
authors.lastname: Nassif
authors.affiliation: Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, USA.
authors.forename: Hassan
authors.initials: H
authors.lastname: Al-Ali
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Miami, Florida, USA.
authors.forename: Sawsan
authors.initials: S
authors.lastname: Khuri
authors.affiliation: Center for Computational Science, University of Miami, Florida, USA.
authors.forename: Walid
authors.initials: W
authors.lastname: Keirouz
authors.affiliation: The Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Florida, USA.
authors.forename: David
authors.initials: D
authors.lastname: Page
keywords: Aleph; ILP; binding site; hexose; protein-carbohydrate interaction; rule generation; substrate recognition