The theoretical average MSE of Δ𝐺 values presented (Fig. ) were calculated based on previously published simulation scripts where expanded details are provided. Optimization in the numeric simulations occurred by finding the design that maximizes the design criteria in Eq. 8 and with methods explained above (Background). The standard deviation of the observation error in 𝚫 Ĝ, 𝜎, was set to 1.0 kcal/mol within the simulations, and errors were assumed to be normally distributed. Briefly, these simulation scripts generate random 𝚫𝐆 𝐓𝐫𝐮𝐞 values, an experimental reference value (Δ𝐺 𝑟𝑒𝑓 ), a weight matrix (𝐖), and a design matrix (𝐀) for all possible transformations (see Background). From these data, we then generated A-optimal, D-optimal, and random designs for varied 𝑛 and 𝑘 using the optimization algorithm describe previously (Software Methods). We solved for 𝚫 Ĝ using weighted linear regression and calculated the variability between all pairs using the variances and covariances of 𝐂. There was one reference ligand per design, and we varied the number of nodes and edges. Finally, we simulated each combination of