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Analysis of structural and functional binding performance of proteins related to genetic basis of diseases is a measure challenge. Podocin protein is a member of flotillin, stomatin and prohibitin, which expressed in nephron tissue. Type 2 nephrotic syndrome (NPHS2) occurs due to mutation in podocin protein. In the present article we have evaluated the binding performance of podocin protein both native as well as mutant with different phytochemicals like aegeline and berberine. We found that aegeline shown better inhibitory effect as compare to berberine against type 2 nephrotic syndrome.