Quality of Approximate Electron Densities and Internal Consistency of Molecular Alignment Algorithms in Molecular Quantum Similarity

The calculation of molecular quantum similarity measures using the molecular electron density requires the
electron density and molecular alignment between two molecules. To obtain meaningful quantum similarity
matrices, the electron density should be calculated efficiently and accurately and the alignment should be
internally consistent. The internal consistency of the alignment for a series of molecules is investigated
through distance geometry concepts. The calculation of the quantum similarity matrix requires the calculation
of a quadratic number of similarity integrals, and a scheme to obtain these efficiently is developed. Both the
alignment procedure and the ASA method for approximate molecular electron densities are tested for a set
of steroid molecules.