In any drug design studies, the protein and ligand interactions are carried out in their lowest energy state, usually selected from protein data bank and the ligands can be either from literature or a database. In such cases, where ligands are derived from literature, certain steps need to be undertaken to perform ‘protein-ligand’ docking studies. Of all the steps involved in ligand docking, the first and foremost major step was energy minimization and conformation search analysis. Different algorithms were used to perform the task. Three major algorithms are considered in this analysis such as Steepest descent, conjugate gradient and block diagonal newton Raphson methods. Here in this paper, we report the utility of such algorithms in minimizing the energies of four anti-diabetic molecules, nateglinide, pioglitazone, repaglinide and glyburide, respectively.