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This article needs additional citations for verification. Please help improve this article by adding citations to reliable sources. Unsourced material may be challenged and removed. Find sources: "PubChem" – news · newspapers · books · scholar · JSTOR (January 2009) (Learn how and when to remove this message)

PubChem

Content
Description	PubChem
Contact
Primary citation	PMID 15879180
Access
Download URL	FTP
Miscellaneous
License	Public domain

PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds. More than 80 database vendors contribute to the growing PubChem database.

Databases

PubChem consists of three dynamically growing primary databases. As of 29 September 2014:

• Compounds, 54 million entries (up from 31 million entries in Jan 2011), contains pure and characterized chemical compounds.
• Substances, 163.5 million entries (up from 75 million entries in Jan 2011), contains also mixtures, extracts, complexes and uncharacterized substances.
• BioAssay, bioactivity results from 6059 (up from 1644 in Jan 2011) high-throughput screening programs with several million values.

Searching

Searching the databases is possible for a broad range of properties including chemical structure, name fragments, chemical formula, molecular weight, XLogP, and hydrogen bond donor and acceptor count.

PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments.

Each hit provides information about synonyms, chemical properties, chemical structure including SMILES and InChI strings, bioactivity, and links to structurally related compounds and other NCBI databases like PubMed.

In the text search form the database fields can be searched by adding the field name in square brackets to the search term. A numeric range is represented by two numbers separated by a colon. The search terms and field names are case-insensitive. Parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used.

Example (Lipinski's Rule of Five):

0:500 0:5 0:10 -5:5

History

PubChem was released in 2004.

ACS's concerns

The American Chemical Society has raised concerns about the publicly supported PubChem database, since it appears to directly compete with their existing Chemical Abstracts Service. They have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the society's revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress.

Soon after PubChem's creation, the American Chemical Society lobbied U.S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service.

Database fields

This section may require cleanup to meet Misplaced Pages's quality standards. No cleanup reason has been specified. Please help improve this section if you can. (November 2009) (Learn how and when to remove this message)

See also

• Chemical database
  • Comparative Toxicogenomics Database
  • ChEMBL
  • ChemSpider
  • eMolecules
  • DrugBank
  • Moltable
  • BindingDB
  • SCRIPDB
• National Center for Biotechnology Information (NCBI)
• Entrez
• PubMed
• GenBank

References

1. "PubChem Source Information". The PubChem Project. USA: National Center for Biotechnology Information.
2. http://www.ncbi.nlm.nih.gov/pccompound?term=all%5Bfilt%5D&cmd=search. Retrieved 29 September 2014. {{cite web}}: Missing or empty |title= (help)
3. "all[filt] - PubChem Compound Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011.
4. "all[filt] - PubChem Substance Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 29 September 2014.
5. "all[filt] - PubChem Substance Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011.
6. "all[filt] - PubChem BioAssay Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 29 September 2014.
7. "all[filt] - PubChem BioAssay Results". The PubChem Project. USA: National Center for Biotechnology Information. Retrieved 7 January 2011.
8. "About PubChem". Retrieved 3 May 2014.
9. Kaiser J (May 2005). "Science resources. Chemists want NIH to curtail database". Science. 308 (5723): 774. doi:10.1126/science.308.5723.774a. PMID 15879180.
10. "PubChem and the American Chemical Society". Reshaping Scholarly Communication. USA: University of California.
11. Cheng T (Nov 2007). "Computation of octanol-water partition coefficients by guiding an additive model with knowledge". Journal of Chemical Information and Modeling. 47 (6): 2140–2148. doi:10.1021/ci700257y. PMID 17985865.

External links

• PubChem homepage
• PubChem searchpage
• PubChem FAQ
• PubChem Help
• PubChemSR Search Aid
• PubChem for Newbies

• Articles needing cleanup from November 2009
• Cleanup tagged articles without a reason field from November 2009
• Misplaced Pages pages needing cleanup from November 2009
• Chemical databases
• Biological databases
• National Institutes of Health