Saint Louis encephalitis virus, a member of the $aviviridae subgroup, is a culex mosquito-borne pathogen. Despite severe epidemic outbreaks on several occasions, not much progress has been made with regard to an epitope-based vaccine designed for Saint Louis encephalitis virus. Covalent binding is an important mechanism for many drugs to gain its function. Computational algorithms to model this chemical event and extended it to a web server have been previously generated. The CovalentDock Cloud provides a simple yet user-friendly web interface to perform covalent docking experiments and analysis online. The web server accepts the structures of both the ligand and the receptor uploaded by the user or retrieved from online databases with valid access id. It identifies the potential covalent binding patterns, carries out the covalent docking experiments and provides visualization of the result for user analysis. Here, in Biogenea we have discovered for the first time a Computational Assay to Design an Epitope-Based Peptide Vaccine Mimo-Peptidic Hyper-Agonist with Mimetic PharmaScaffold chemical agents comprising vaccine like properties Against Saint Louis Encephalitis Virus. These novel hyperstructures were generated by Using the BiogenetoligandorolTM AND the CovalentDock Cloud: a web server for automated covalent docking.