- Article -
| In Silico Biology 7, 0037 (2007); ©2007, Bioinformation Systems e.V. |
BETTY: Prediction of β-strand type from sequence
Olav Zimmermann1*, Longhui Wang1 and Ulrich H. E. Hansmann1,2
1 John v. Neumann Institute for Computing, FZ Jülich, 52425 Jülich, Germany
2 Dept. of Physics, Michigan Technological University, Houghton, MI 49931-1295, USA
* Corresponding author
Email: olav.zimmermann@fz-juelich.de
Edited by H. Michael; received April 18, 2007; revised July 01, 2007; accepted July 05, 2007; published August 28, 2007
Abstract
Most secondary structure prediction programs do not distinguish between parallel and antiparallel β-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 β-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.
Keywords: SVM, support vector machine, structure prediction, secondary structure prediction, tertiary structure prediction, beta-sheets, beta-strands, parallel beta-sheets, antiparallel beta-sheets, long range constraints