Although the use of 3-D similarity techniques in the analysis of biological data and virtual screening is pervasive, little has been known about the statistical meaning of similarity scores from these methods.  To address this issue, the similarity value distribution curves for randomly selected compounds were generated using six different 3-D similarity types utilized by PubChem analysis tools.  An attempt was also made to explore the question of whether it was possible to realize a statistically meaningful 3-D similarity value separation between reputed biological assay actives and inactives.  In addition, the complementarity between PubChem's 2-D and 3-D similarity methods was investigated.  This work is a critical step to create a statistical framework to build upon and will help to develop search and analysis tools that exploit 3-D molecular similarity.

Statistical significance of 3D molecular similarity scores

244th National Meeting (2012)

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