BETTY: prediction of beta-strand type from sequence

In Silico Biol. 2007;7(4-5):535-42.

Abstract

Most secondary structure prediction programs do not distinguish between parallel and antiparallel beta-sheets. However, such knowledge would constrain the available topologies of a protein significantly, and therefore aid existing fold recognition algorithms. For this reason, we propose a technique which, in combination with existing secondary structure programs such as PSIPRED, allows one to distinguish between parallel and antiparallel beta-sheets. We propose the use of a support vector machine (SVM) procedure, BETTY, to predict parallel and antiparallel sheets from sequence. We found that there is a strong signal difference in the sequence profiles which SVMs can efficiently extract. With strand type assignment accuracies of 90.7% and 83.3% for antiparallel and parallel strands, respectively, our method adds considerably to existing information on current 3-class secondary structure predictions. BETTY has been implemented as an online service which academic researchers can access from our website http://www.fz-juelich.de/nic/cbb/service/service.php.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • Amino Acid Motifs*
  • Amino Acid Sequence
  • Artificial Intelligence*
  • Models, Molecular
  • Protein Folding
  • Protein Structure, Secondary*