In Silico Analysis for Determination and Validation of Human CD20 Antigen 3D Structure

CD20 has been known as an attractive therapeutic target for refractory diseases such as B-cell chronic lymphocytic leukemia, rheumatoid arthritis and multiple sclerosis. Determining the 3D structure of the CD20 antigen could help to achieve a better deduction of its functions and its interactions with ligands. In this regard, we have launched an in silico protein modeling strategy to unveil the probable 3D structure of CD20 molecule. Various protein modeling approaches including homology modeling, Fold recognition and ab initio method were employed to build a qualified mode Protein BLAST tool from NCBI database was used to find a suitable template and the selected template was fed as input structure of the modeling software. Thereafter, the quality of the obtained models was evaluated invoking the model quality assessment software. CD20 Topology prediction shows that 4 trans membrane helixes. The best model predicted by LOMETS was selected for analyses. Refinement of 3D structure as well as determination of its B-cell epitopes, clefts and ligand binding sites was carried out on the structure. In conclusion, CD20 antigen 3D prediction led to design and production of a new monoclonal antibody.