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Automatic comparative molecular modelling of viral coat protein performs the homology modelling in different steps. Protein sequence of Capsid protein (Cucumber mosaic virus strain As) shows identify homologous proteins with known 3D structures by using PSI-BLAST i.e. it shows similarity with capsid protein from Cucumber mosaic virus (strain fny). Through analysis we got Nucleoplasmin-like viral coat protein as a potential template through a very convenient user interface for target selection. Bioinformatics software tools can reveal in formation on many aspect of protein structure and function, such as protein interaction expression pattern, surface activity, binding sites, and electrostatic potentials. Study focused on computational approach to deciphering the sequence similarity, molecular modeling and their function of coat protein of cucumber mosaic virus (strain fny). The data generated from these assay is subsequently added to a searchable database that allows potential drug targets to identify.