Work on the HBV core protein of Hepatitis B has been performed in order to have deep considerate of the structure of this virulent protein. To understand the underlying mechanism and to see the effect of different drugs on it by using different bioinformatics tools. The proposed work has been divided into two stages, building model of the protein structure through the use of bioinformatics tools and then the designing and docking of the proposed drugs. All steps of homology modeling and refinement were carried out by the program MODELLER (Version 9 (9v8)). The law of PROCHECK is to estimate the overall stereo-chemical value of a given model and Energy of protein folds was finding out by using the tool ProSA (Protein Structure Analysis, Version.4). Docking server and DS viewer were used to study the inter actions of the ligands with the protein. Molecular docking server Interaction of the ligand with the protein in terms hydrophobic interactions, hydrophilic interactions and other interactions. Hex dock server helped in binding the ligand with the protein. The 17 residues are conserved in pair wise alignment between target and template. All the sequences shows highest similarity when these sequences were loaded into CUSTAL X. Tertiary structure of HBV core consist of two main domains A+B structure topology. The Alanine shows same interaction between hex and molecular docking server with Tenofovir, Telbivudine, Lamivudine drugs. The tryptophan and Alanine shows same interaction with Tenofovir, Telbivudine, Lamivudine drugs in molecular docking.