Improved detection of helix-turn-helix DNA-binding motifs in protein sequences

Nucleic Acids Res. 1990 Sep 11;18(17):5019-26. doi: 10.1093/nar/18.17.5019.


We present an update of our method for systematic detection and evaluation of potential helix-turn-helix DNA-binding motifs in protein sequences [Dodd, I. and Egan, J. B. (1987) J. Mol. Biol. 194, 557-564]. The new method is considerably more powerful, detecting approximately 50% more likely helix-turn-helix sequences without an increase in false predictions. This improvement is due almost entirely to the use of a much larger reference set of 91 presumed helix-turn-helix sequences. The scoring matrix derived from this reference set has been calibrated against a large protein sequence database so that the score obtained by a sequence can be used to give a practical estimation of the probability that the sequence is a helix-turn-helix motif.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • DNA / metabolism*
  • DNA-Binding Proteins / metabolism*
  • Information Systems
  • Molecular Sequence Data
  • Probability
  • Protein Conformation


  • DNA-Binding Proteins
  • DNA