Rapid evaluation of molecular shape similarity index using pairwise calculation of the nearest atomic distances

Rapid evaluation method for obtaining molecular shape similarity index using pairwise calculation of the nearest atomic distance respected to the template atoms was investigated. This method for calculations of similarity indices remarkably reduced required time compared with hitherto methods (especially 2 or 3 orders of magnitude faster than the previous grid-based evaluation technique) and gave without clear loss of preciseness. The potential of these improvements and possible further enhancements are discussed.