Algorithm improvement for the molecular-shape analysis reflecting electronic interactions and its application to molecular similarity among bioisosteres.

Abstract

We improved a method of molecular-shape analysis developed in our group. We tried to automate a procedure consisting of several independent tasks. In addition, the computational cost was largely reduced by restricting the sampling points within a sphere centered on each atom. The efficiency was confirmed through applications to water molecule: the number of sampling points was reduced to a quarter of the initial set. By this improvement, application to large molecules has become possible at low cost. The improved algorithm was applied to investigate molecular similarity among bioisosteres suggested empirically. The similarity was numerically evaluated by referring to interaction between an ion probe and a target molecule.