Dataset Information
Learning biophysically-motivated parameters for alpha helix prediction.
Ontology highlight
ABSTRACT: Background
Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.Results
Focusing on the prediction of alpha helices in proteins, we show that a model with 302 parameters can achieve a Qalpha value of 77.6% and an SOValpha value of 73.4%. Such performance numbers are among the best for techniques that do not rely on external databases (such as multiple sequence alignments). Further, it is easier to extract biological significance from a model with so few parameters.Conclusion
The method presented shows promise for the prediction of protein secondary structure. Biophysically-motivated elementary free-energies can be learned using SVM techniques to construct an energy cost function whose predictive performance rivals state-of-the-art. This method is general and can be extended beyond the all-alpha case described here.
SUBMITTER: Gassend B
PROVIDER: S-EPMC1892091 | biostudies-literature | 2007 May
REPOSITORIES: biostudies-literature
Publications
Learning biophysically-motivated parameters for alpha helix prediction.
BMC bioinformatics 20070524
<h4>Background</h4>Our goal is to develop a state-of-the-art protein secondary structure predictor, with an intuitive and biophysically-motivated energy model. We treat structure prediction as an optimization problem, using parameterizable cost functions representing biological "pseudo-energies". Machine learning methods are applied to estimate the values of the parameters to correctly predict known protein structures.<h4>Results</h4>Focusing on the prediction of alpha helices in proteins, we sh ...[more]
