Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems. In our study, advanced computational technique such as MD simulation using "Schrodinger" package have been used to study heat shock protein (Hsp90) of plant origin. The protocol has been discussed in detail so as to assist other people working in similar areas, particularity in plant sciences, to initiate research in the exciting field of bioinformatics.