PubChem3D: Diversity of shape
<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2011-03-01
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| Series: | Journal of Cheminformatics |
| Online Access: | http://www.jcheminf.com/content/3/1/9 |
| _version_ | 1811284973422903296 |
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| author | Bolton Evan E Kim Sunghwan Bryant Stephen H |
| author_facet | Bolton Evan E Kim Sunghwan Bryant Stephen H |
| author_sort | Bolton Evan E |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-13T02:37:37Z |
| format | Article |
| id | doaj.art-5885cf9aba834255bfd557c5ca05e41f |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-04-13T02:37:37Z |
| publishDate | 2011-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-5885cf9aba834255bfd557c5ca05e41f2022-12-22T03:06:20ZengBMCJournal of Cheminformatics1758-29462011-03-0131910.1186/1758-2946-3-9PubChem3D: Diversity of shapeBolton Evan EKim SunghwanBryant Stephen H<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.jcheminf.com/content/3/1/9 |
| spellingShingle | Bolton Evan E Kim Sunghwan Bryant Stephen H PubChem3D: Diversity of shape Journal of Cheminformatics |
| title | PubChem3D: Diversity of shape |
| title_full | PubChem3D: Diversity of shape |
| title_fullStr | PubChem3D: Diversity of shape |
| title_full_unstemmed | PubChem3D: Diversity of shape |
| title_short | PubChem3D: Diversity of shape |
| title_sort | pubchem3d diversity of shape |
| url | http://www.jcheminf.com/content/3/1/9 |
| work_keys_str_mv | AT boltonevane pubchem3ddiversityofshape AT kimsunghwan pubchem3ddiversityofshape AT bryantstephenh pubchem3ddiversityofshape |