Title |
PubChem3D: Conformer generation
|
---|---|
Published in |
Journal of Cheminformatics, January 2011
|
DOI | 10.1186/1758-2946-3-4 |
Pubmed ID | |
Authors |
Evan E Bolton, Sunghwan Kim, Stephen H Bryant |
Abstract |
PubChem, an open archive for the biological activities of small molecules, provides search and analysis tools to assist users in locating desired information. Many of these tools focus on the notion of chemical structure similarity at some level. PubChem3D enables similarity of chemical structure 3-D conformers to augment the existing similarity of 2-D chemical structure graphs. It is also desirable to relate theoretical 3-D descriptions of chemical structures to experimental biological activity. As such, it is important to be assured that the theoretical conformer models can reproduce experimentally determined bioactive conformations. In the present study, we investigate the effects of three primary conformer generation parameters (the fragment sampling rate, the energy window size, and force field variant) upon the accuracy of theoretical conformer models, and determined optimal settings for PubChem3D conformer model generation and conformer sampling. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Hungary | 1 | 50% |
Unknown | 1 | 50% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 2 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 3 | 4% |
Germany | 2 | 3% |
France | 1 | 1% |
Sri Lanka | 1 | 1% |
Czechia | 1 | 1% |
Japan | 1 | 1% |
Russia | 1 | 1% |
Unknown | 66 | 87% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 24 | 32% |
Student > Ph. D. Student | 11 | 14% |
Other | 7 | 9% |
Student > Bachelor | 6 | 8% |
Student > Doctoral Student | 4 | 5% |
Other | 15 | 20% |
Unknown | 9 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Chemistry | 24 | 32% |
Agricultural and Biological Sciences | 13 | 17% |
Computer Science | 7 | 9% |
Materials Science | 6 | 8% |
Medicine and Dentistry | 4 | 5% |
Other | 11 | 14% |
Unknown | 11 | 14% |