Biophysics is the study of living systems in terms of concept and laws of physics. So it is an inter disciplinary subject. Biophysics is simply the application of physics to biology. At the simplest level, one finds that one can apply physics in understanding the working of organ system. At the next level, Biophysics attempts to understand the structure, this aspect deals with the study of molecular biology. Here, We build a three dimensional model of a new protein [Green Sea Turtle] based on the knowledge of the solved protein structure {Sperm whale], which have the similar sequence of a new protein. Then verify our model by using various analysis tools. Molecular modelling is done by X-ray crystallography, NMR and other physical methods are the time consuming factors, our aim to overcome the time factor, so we choose computer package to do this HOMOLOGY MODELING.In this case of Homology modelling between green sea turtle and sperm whale, i) Energy Minimizationii) Quality Checkiii) Ramachandran Plot are discussed