The intelligent engineering of antibodies for the specific recognition of heavy metal complex antigens via single site mutations is a key step in the development of antibody based biosensors for the testing of contaminated soils and water streams. The recognition subunit of the antibody is composed of a heavy and light chain sequence, which come together to form the binding pocket. The pocket region is surrounded by six highly variable loops (3 heavy chain and 3 light chain loops) which confer binding specificity to the antibody. Using molecular simulations, we characterize the loop regions to determine which amino acid side chains most likely contribute to heavy metal complex binding for antibody 5B2 described in Delehanty et al., Biochemistry 2003, 42. The loop region is known to be relatively inflexible over the time scales (~10 ns) of brute force molecular dynamics calculations. We therefore employ advanced Replica Exchange techniques to more exhaustively explore the loop conformations. Harvesting configurations generated from these simulations, we minimize their potential energies to characterize the underlying inherent structures of the loops. These calculations yield insight into the residues closest to the binding pocket and allow us, in collaboration with our experimental colleagues, to suggest those amino acids which can be manipulated to more time efficiently optimize the binding affinity of Pb(II)-DTPA complexes to 5B2.