Antigenic: An improved prediction model of protective antigens

Abstract

An antigen is a protein capable of triggering an effective immune system response. Protective antigens are the ones that can invoke specific and enhanced adaptive immune response to subsequent exposure to the specific pathogen or related organisms. Such proteins are therefore of immense importance in vaccine preparation and drug design. However, the laboratory experiments to isolate and identify antigens from a microbial pathogen are expensive, time consuming and often unsuccessful. This is why Reverse Vaccinology has become the modern trend of vaccine search, where computational methods are first applied to predict protective antigens or their determinants, known as epitopes. In this paper, we propose a novel, accurate computational model to identify protective antigens efficiently. Our model extracts features directly from the protein sequences, without any dependence on functional domain or structural information. After relevant features are extracted, we have used Random Forest algorithm to rank the features. Then Recursive Feature Elimination (RFE) and minimum redundancy maximum relevance (mRMR) criterion were applied to extract an optimal set of features. The learning model was trained using Random Forest algorithm. Named as Antigenic, our proposed model demonstrates superior performance compared to the state-of-the-art predictors on a benchmark dataset. Antigenic achieves accuracy, sensitivity and specificity values of 78.04%, 78.99% and 77.08% in 10-fold cross-validation testing respectively. In jackknife cross-validation, the corresponding scores are 80.03%, 80.90% and 79.16% respectively. The source code of Antigenic, along with relevant dataset and detailed experimental results, can be found at https://github.com/srautonu/AntigenPredictor. A publicly accessible web interface has also been established at: http://antigenic.research.buet.ac.bd.