PubChem3D: Diversity of shape

By Evan E. Bolton, Sunghwan Kim, Stephen H. Bryant. 2011

14 citations recorded by the source corpus.

BackgroundThe 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.ResultsThe 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.ConclusionThe 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.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Spectroscopy

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Citations in the corpus

PubChem3D: a new resource for scientists (2011, methodology): “The sampling procedure employed is described else-where [7] but involves a two-stage clustering approach with an initial pass to partition-cluster conformers using an exclusion region hierarchy of decreasing dissimilarity (NlogN computational complexity, each cluster representative forms an…”
PubChem3D: conformer ensemble accuracy (2013, methodology): “The conformers in each conformer ensemble were down-sampled using a partition-based clustering scheme, as described in our previous study [15], with the RMSD as a distance threshold between conformers (that is, RMSD) and”
PubChem3D: Biologically relevant 3-D similarity (2011, background): “The PubChem3D project [22-25], launched, in part, to help users identify useful structure-activity relationships, generates a theoretical 3-D conformer model [22,23] for each molecule in the PubChem Compound database, whenever it is possible.”
PubChem3D: Shape compatibility filtering using molecular shape quadrupoles (2011, background): “D layer, PubChem3D [5-7], which provides a precomputed 3-”
Effects of multiple conformers per compound upon 3-D similarity search and bioassay data analysis (2012, methodology): “The PubChem3D project [5-11] augments the utility of PubChem, by adding computed three-dimensional (3-D) descriptions to about 90% of the small molecules contained in the PubChem Compound database [6,11].”
PubChem3D: Similar conformers (2011, methodology): “However, when examining the growth of shape space per unit volume for a maximum count of reference shapes [15], shape space was shown to grow gradually and smoothly as a function of ST.”