Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif

William A. McLaughlin, Helen M. Berman

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

A method for discerning protein structures containing the DNA-binding helix-turn-helix (HTH) motif has been developed. The method uses statistical models based on geometrical measurements of the motif. With a decision tree model, key structural features required for DNA binding were identified. These include a high average solvent-accessibility of residues within the recognition helix and a conserved hydrophobic interaction between the recognition helix and the second alpha helix preceding it. The Protein Data Bank was searched using a more accurate model of the motif created using the Adaboost algorithm to identify structures that have a high probability of containing the motif, including those that had not been reported previously.

Original languageEnglish (US)
Pages (from-to)43-55
Number of pages13
JournalJournal of molecular biology
Volume330
Issue number1
DOIs
StatePublished - Jun 27 2003

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Molecular Biology

Keywords

  • DNA-binding
  • Helix-turn-helix motif
  • Machine learning
  • Structure classification

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