Sunghwan Kim - PubChem3D: Diversity of shape

Version 2

      Publication Details (including relevant citation   information):

      E.E. Bolton, S.   Kim, and S.H. Bryant;

      Journal of Cheminformatics, 2011, 3, 9.




      The shape diversity of 16.4 million biologically relevant   molecules from the PubChem Compound database and their 1.46   billion diverse conformers was explored as a function of   molecular volume.


      The diversity of shape space was investigated by determining the   shape similarity threshold to achieve a maximum on the count of   reference shapes per unit of conformer volume. The rate of growth   in shape space, as represented by a decreasing shape similarity   threshold, was found to be remarkably smooth as a function of   volume. There was no apparent correlation between the count of   conformers per unit volume and their diversity, meaning that a   single reference shape can describe the shape space of many   chemical structures. The ability of a volume to describe the   shape space of lesser volumes was also examined. It was shown   that a given volume was able to describe 40-70% of the shape   diversity of lesser volumes, for the majority of the volume range   considered in this study.


      The relative growth of shape diversity as a function of volume   and shape similarity is surprisingly uniform. Given the   distribution of chemicals in PubChem versus what is theoretically   synthetically possible, the results from this analysis should be   considered a conservative estimate to the true diversity of shape   space.


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