MCP: a Multi-Component learning machine to Predict protein secondary structure

Abstract

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is tightly connected to its specific 3D structure. Prediction of the protein secondary structure is a crucial intermediate step towards elucidating its 3D structure and function. Traditional experimental methods for prediction of protein structure are expensive and time-consuming. Therefore, various machine learning approaches have been proposed to predict the protein secondary structure. Nevertheless, the average accuracy of the suggested solutions has hardly reached beyond 80%. The possible underlying reasons are the ambiguous sequence-structure relation, noise in input protein data, class imbalance, and the high dimensionality of the encoding schemes that represent the protein sequence. In this paper, we propose an accurate multi-component prediction machine to overcome the challenges of protein structure prediction. We devise a multi-component designation to address the high complexity challenge in sequence-structure relation. Furthermore, we utilize a compound string dissimilarity measure to directly interpret protein sequence content and avoid information loss. In order to improve the accuracy, we employ two different classifiers including support vector machine and fuzzy nearest neighbor and collectively aggregate the classification outcomes to infer the final protein secondary structures. We conduct comprehensive experiments to compare our model with the current state-of-the-art approaches. The experimental results demonstrate that given a set of input sequences, our multi-component framework can accurately predict the protein structure. Nevertheless, the effectiveness of our unified model an be further enhanced through framework configuration.