Statistical models for discerning protein structures containing the DNA-binding helix-turn-helix motif.
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.
McLaughlin
William A
WA
Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway 08854-8087, USA.
Berman
Helen M
HM
D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D030562:Databases, Protein; D003663:Decision Trees; D019077:Helix-Turn-Helix Motifs; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
D004268:DNA-Binding Proteins; D011506:Proteins; D004247:DNA