Acquisition of rule-based knowledge for analyzing DNA-binding sites in proteins

Shinn Jang Ho, Chia Yun Chang, Liang Tsung Huang, Shiow Fen Hwang, Shinn-Ying Ho

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

1 Scopus citations

Abstract

This study aims to analyze DNA-binding proteins via acquisition of interpretable knowledge which can accurately predict binding sites in proteins to understand DNA-protein recognition mechanism. For mining accurate and interpretable knowledge, a large-scale dataset consisting of 982 DNA-binding proteins is constructed. This study investigates a novel feature set consisting of 11 features, including solvent accessibility, secondary structure, charge information near the residue, amino acid group and neighbor property. The derived binding and non-binding rules reveal that besides the well-known solvent accessibility, the electric charge distribution near the residue and the amino acid groups also play important roles in prediction of binding sites. The interpretable and accurate knowledge is helpful for biologist to analyze DNA-binding proteins.

Original languageEnglish
Title of host publicationProceedings of the 2nd International Conference on Scalable Information Systems, InfoScale 2007
PublisherAssociation for Computing Machinery
ISBN (Electronic)9781595937575
DOIs
StatePublished - 6 Jun 2007
Event2nd International Conference on Scalable Information Systems, InfoScale 2007 - Suzhou, China
Duration: 6 Jun 20078 Jun 2007

Publication series

NameACM International Conference Proceeding Series
Volume06-08-June-2007

Conference

Conference2nd International Conference on Scalable Information Systems, InfoScale 2007
CountryChina
CitySuzhou
Period6/06/078/06/07

Keywords

  • Binding site
  • Decision tree
  • Knowledge acquisition
  • Protein

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