A knowledge-based potential scoring function, named M-Score, has been developed based upon 2331 high-resolution crystal structures of protein-ligand complexes. M-Score considers the mobility of protein atoms, describing the location of each protein atom by a Gaussian distribution instead of a fixed position based upon the isotropic B-factors. This leads to an increase in the number of atom-pairs in the construction of knowledge-based potentials and a smoothing effect on the pairwise distribution functions. M-Score was validated using 896 complexes which were not included in the 2331 data set and whose experimentally determined binding affinities were available. The overall linear correlation coefficient (r) between the calculated scores and experimentally determined binding affinities (pKi or pKd) for these 896 complexes is -0.49. Evaluation of M-Score against 17 protein families showed that we obtained good to excellent correlations for six protein families, modest correlations for four protein families, and poor correlations for the remaining seven protein families.