PubChem3D: a new resource for scientists
| Autor: | Stephen H. Bryant, Siqian He, Paul A. Thiessen, Evan E Bolton, Bo Yu, Sunghwan Kim, Wenyao Shi, Lianyi Han, Jian Zhang, Yan Sun, Jiyao Wang, Jie Chen, Vahan Simonyan |
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| Jazyk: | angličtina |
| Rok vydání: | 2011 |
| Předmět: |
Exploit
lcsh:T58.5-58.64 Computer science lcsh:Information technology Scale (chemistry) computer.file_format Library and Information Sciences computer.software_genre Computer Graphics and Computer-Aided Design Visualization Computer Science Applications Set (abstract data type) lcsh:Chemistry Similarity (network science) lcsh:QD1-999 Atom (standard) Data mining Layer (object-oriented design) Physical and Theoretical Chemistry computer Software PubChem |
| Zdroj: | Journal of Cheminformatics, Vol 3, Iss 1, p 32 (2011) Journal of Cheminformatics |
| ISSN: | 1758-2946 |
| Popis: | Background PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis. Description PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data. A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity. Conclusions The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem. |
| Databáze: | OpenAIRE |
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