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Updated: Aug 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif
William A McLaughlin1, Helen M Berman
1Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway 08854-8087, USA.
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.
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