Predicting conformational switches in proteins

Malin Young, Kent Kirshenbaum, Ken A. Dill, Stefan Highsmith

Research output: Contribution to journalArticlepeer-review


We describe a new computational technique to predict conformationally switching elements in proteins from their amino acid sequences. The method, called ASP (Ambivalent Structure Predictor), analyzes results from a secondary structure prediction algorithm to identify regions of conformational ambivalence. ASP identifies ambivalent regions in 16 test protein sequences for which function involves substantial backbone rearrangements. In the test set, all sites previously described as conformational switches are correctly predicted to be structurally ambivalent regions. No such regions are predicted in three negative control protein sequences. ASP may be useful as a guide for experimental studies on protein function and motion in the absence of detailed three-dimensional structural data.

Original languageEnglish (US)
Pages (from-to)1752-1764
Number of pages13
JournalProtein Science
Issue number9
StatePublished - 1999


  • ASP
  • Conformational switch
  • PHD
  • Secondary structure preferences
  • Structurally ambivalent sequence element

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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