Structure based computational approaches are desirable to recognize and characterize protein-protein complexes and their functions. For specific proteins, the supreme fruitful technique is homology modeling whereas docking algorithms are progressively powerful and can deliver a detailed explanation of the interaction. Previous studies on modeling of hyda2 were based on different template models (Anabaena 7119 chain A, spinach PDB code 1A70, PDB code 1CZP, and Anabaena 7120 PDB code 1FRD) (Chang et al. 2007). Model produced from these templates are not considered suitable for interaction with petf as template used in these models are unmatured hydrogenase. Furthermore it was seen that, the Fe-Fe active site was not inserted due to the missing of HydE/F/G genes (Mulder et al. 2010).