The evaluation of the electron density based similarity function scales quadratically with respect to the size of the molecules for simplified, atomic shell densities. Due to the exponential decay of the function’s atom-atom terms most interatomic contributions are numerically negligible on large systems. An improved algorithm for the evaluation of the Molecular Quantum Similarity function is presented. This procedure identifies all non-negligible terms without computing unnecessary interatomic squared distances, thus effectively turning to linear scaling the similarity evaluation. Presented also is a minimalist dynamic electron density model. Approximate, single shell densities together with the proposed algorithm facilitate fast electron density based alignments on macromolecules.