Molecular docking was carried out against two target proteins which are helpful for MRSA infection with the help of accelrys discovery studio to understand the applicability of the method to differentiate between the active and inactive compounds. Molecular docking of thirty two structurally diverse inhibitors were carried out and it was observed that though some false positives were also obtained; considering the limitations of the available docking programs, the results were promising. The high molecular weight compounds with heterocyclic rings showed very low binding energy, but did not comply with Lipinski's rule. The active constituents that were docked with the protein are Baicalein, Biochanin, Carnosol, Genistein, Orobol, Resveratrol, Rhein, Gallic acid, Pyrithione, Resveratrol and Linozolid .The compound Orobol was found to interact more towards the target protein like showing highest Dock score.