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PubChem

Content
Description	PubChem
Contact
Primary citation	PMID 15879180
Access
Download URL	FTP
Tools
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. The American Chemical Society tried to get the U.S. Congress to restrict the operation of PubChem, because they claim it competes with their Chemical Abstracts Service.^[1] More than 80 database vendors contribute to the growing PubChem database.^[2]

Databases [edit]

PubChem consists of three dynamically growing primary databases. As of 7 January 2011:

• Compounds, 31 million entries, contains pure and characterized chemical compounds.^[3]
• Substances, 75 million entries, contains also mixtures, extracts, complexes and uncharacterized substances.^[4]
• BioAssay, bioactivity results from 1644 high-throughput screening programs with several million values.^[5]

Searching [edit]

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[mw] 0:5[hbdc] 0:10[hbac] -5:5[logp]

ACS's concerns [edit]

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.^[6] 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.

Database fields [edit]

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See also [edit]

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

References [edit]

External links [edit]

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