We applied the method to two protein-fragment systems, T4L99A and MUP1, to enhance traditional MSMD simulations. In both cases, we assumed no prior knowledge of the binding region and subsequently ran GCNCMC simulations to generate a set of possible binding sites. We conducted a comparative analysis between GCNCMC and a basic MSMD protocol, revealing that GCNCMC readily identified experimental binding sites in both systems, whereas MSMD did not.