Margin-based ensemble classifier for protein fold recognition

Recognition of protein folding patterns is an important step in protein structure and function predictions. Traditional sequence similarity-based approach fails to yield convincing predictions when proteins have low sequence identities, while the taxonometric approach is a reliable alternative. From a pattern recognition perspective, protein fold recognition involves a large number of classes with only a small number of training samples, and multiple heterogeneous feature groups derived from different propensities of amino acids. This raises the need for a classification method that is able to handle the data complexity with a high prediction accuracy for practical applications. To this end, a novel ensemble classifier, called MarFold, is proposed in this paper which combines three margin-based classifiers for protein fold recognition.The effectiveness of our method is demonstrated with the benchmark D-B dataset with 27 classes. The overall prediction accuracy obtained by MarFold is 71.7%, which surpasses the existing fold recognition methods by 3.1–15.7%. Moreover, one component classifier for MarFold, called ALH, has obtained a prediction accuracy of 65.5%, which is 4.7–9.5% higher than the prediction accuracies for the published methods using single classifiers. Additionally, the feature set of pairwise frequency information about the amino acids, which is adopted by MarFold, is found to be important for discriminating folding patterns. These results imply that the MarFold method and its operation engine ALH might become useful vehicles for protein fold recognition, as well as other bioinformatics tasks. The MarFold method and the datasets can be obtained from: (http://www-staff.it.uts.edu.au/∼lbcao/publication/MarFold.7z).

► Recognition of protein folding patterns is an important step in protein structure and function predictions.
► A novel ensemble classifier, called MarFold, is proposed in this paper which combines three margin-based classifiers for protein fold recognition.
► MarFold method and its operation engine ALH might become useful vehicles for protein fold recognition, as well as other bioinformatics tasks.