PubChem: a public information system for analyzing bioactivities of small molecules

By Yanli Wang, Jewen Xiao, Tugba Onal Suzek, Jian Zhang, Jiyao Wang, Stephen H. Bryant. 2009

1,424 citations recorded by the source corpus.

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological properties of small molecules hosted by the US National Institutes of Health (NIH). PubChem BioAssay database currently contains biological test results for more than 700 000 compounds. The goal of PubChem is to make this information easily accessible to biomedical researchers. In this work, we present a set of web servers to facilitate and optimize the utility of biological activity information within PubChem. These web-based services provide tools for rapid data retrieval, integration and comparison of biological screening results, exploratory structure–activity analysis, and target selectivity examination. This article reviews these bioactivity analysis tools and discusses their uses. Most of the tools described in this work can be directly accessed at http://pubchem.ncbi.nlm.nih.gov/assay/. URLs for accessing other tools described in this work are specified individually.

Subfields: Computational Theory and Mathematics, Pharmacology

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Citations in the corpus

An overview of the PubChem BioAssay resource (2009, methodology): “gov) (1,2) (Figure 1) is an open public repository containing chemical structures and biological properties of molecules including small molecules and siRNA reagents.”
Chemical Entities of Biological Interest: an update (2009, methodology): “Furthermore, searches can be filtered by database; for example, one can search for entities used in the NMRShiftDB (5) or PubChem (6) databases.”
The Comparative Toxicogenomics Database: update 2011 (2010, background): “The value and utility of CTD is evidenced by it being indexed at numerous other databases, including PubChem (6), PharmGKB (7), UniProt (8), T3DB (9), GAD (10) and ChemID (11), and by the inclusion of CTD’s curated information in other database products, such as STITCH (12), ToppGene (13), PhenoHM (”
Database resources of the National Center for Biotechnology Information (2010, background): “PubChem (65) is the informatics backbone for the NIH Roadmap Initiative on molecular libraries and focuses on the chemical, structural and biological properties of small molecules, in particular their roles as diagnostic and therapeutic agents.”
PubChem3D: Conformer generation (2011, background): “PubChem [1-4] is an open archive for the biological activities of small molecules.”
BindingDB in 2015: A public database for medicinal chemistry, computational chemistry and systems pharmacology (2015, background): “Similarly, only confirmatory assay re-sults are collected from PubChem, as these are actual affinity data derived from proper compound titrations.”
Visualisation and subsets of the chemical universe database GDB-13 for virtual screening (2011, methodology): “The analysis produces meaningful overviews of large molecular databases such as ZINC [23] and PubChem [9] as color-coded maps derived from principal component analysis (PCA) of the MQN data [24].”
Network pharmacology: towards the artificial intelligence-based precision traditional Chinese medicine (2023, background): “…of drugs/formulas, the structural similarity relationships between the components contained in formulas are mainlyminedfromdatabasessuchasPubChem[24],ChEMBL[25], CDCDB [26] and DrugCombDB [27], as well as the relationships between the herbs contained in formulas and their properties (e.g.…”
PubChem3D: Diversity of shape (2011, methodology): “Conformers were generated for chemical structures in the PubChem Compound database[15-18] as described in the Materials and Methods section.”
PubChem3D: a new resource for scientists (2011, neutral): “PubChem [1-4](http://pubchem.”