Similarity searching in databases of flexible 3D structures using smoothed bounded distance matrices

This paper describes a method for calculating the similarity between pairs of chemical structures represented by 3D molecular graphs. The method is based on a graph matching procedure that accommodates conformational flexibility by using distance ranges between pairs of atoms, rather than fixing the atom pair distances. These distance ranges are generated using triangle and tetrangle bound smoothing techniques from distance geometry. The effectiveness of the proposed method in retrieving other compounds of like biological activity is evaluated, and the results are compared with those obtained from other, 2D-based methods for similarity searching.