Performing these methods allowed us to investigate how much sampling would be needed for reproducible results. These calculations on PTP1B and the PDZ3 domain were performed in the same manner, by using the per residue scores obtained from the Jensen-Shannon distance metric. First, the complete datasets were separated into their individual 20 replicas, with PTP1B having 10 replicas from both the "closed" and "open" WPD-loop conformations, and the PDZ3 domain having 10 replicas from both the "bound" and "unliganded" states. For the different scenarios to bootstrap or sub sample from, a random selection of X replicas (where X was either 1, 2, 3, 5, 8 or 10) from both states were extracted (giving 2, 4, 6, 10, 16 or 20 replicas in total respectively) and the per residue scores were determined for each sample.