Antigenic: An improved prediction model of protective antigens

Publication date: Available online 3 January 2019Source: Artificial Intelligence in MedicineAuthor(s): M. Saifur Rahman, Md. Khaledur Rahman, Sanjay Saha, M. Kaykobad, M. Sohel RahmanAbstractAn 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 perfor...
Source: Artificial Intelligence in Medicine - Category: Bioinformatics Source Type: research

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