PubChem

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PubChem
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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

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

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

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.[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

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Identification numbers
• Identification number in current database [UID]
• Substance identification number [SID]
• Compound identification number [CID]
• BioAssay identification number [BAID], [AID]

General
• Any database field [ALL]
• Comment [CMT]
• Deposition date [DDAT], [DEPDAT]
• Depositor's external ID [SRID], [SRCID]
• Source name [SRC], [SRCNAM], [SRCNAME]
• Source release date [SRD], [SRDAT], [RLSDAT]
• Medical Subject Heading (MeSH) term [MSHT], [MESHT]
• MeSH tree node [MSHN], [MESHTN]
• MeSH pharmacological actions [PHMA], [PHARMA]

Substance properties
• Substance synonyms [SYNO]
• IUPAC name [UPAC], [IUPAC]
• International Chemical Identifier (InChI) [INCHI]
• Molecular weight [MW], [MWT], [MOLWT]
• Chemical elements [ELMT], [EL]
• Non-Hydrogen atoms [HAC], [HACNT]
• Isotope count [IAC], [IACNT]
• Total formal charge [TFC], [CHG], [CHRG]
• Chiral atom count [ACC], [ACCNT]
• Defined chiral atom count [ACDC], [ACDCNT]
• Undefined chiral atom count [ACUC], [ACUCNT]
• Hydrogen bond acceptor count [HBAC], [HBACNT]
• Hydrogen bond donor count [HBDC], [HBDCNT]
• Tautomer count [TC], [TCNT], [TTMC]
• Rotatable bond count [RBC], [RBCNT]
• XLogP [XLGP], [LOGP]

Compound properties
• Compound synonyms [CSYN], [CSYNO]
• Component count [CC], [CCNT]
• Covalent unit (molecule) count [CUC], [CUCNT]
• Total bioactivity count [TAC]

See also

References

  1. ↑ "PubChem and the American Chemical Society". Reshaping Scholarly Communication. USA: University of California. http://osc.universityofcalifornia.edu/news/acs_pubchem.html.
  2. ↑ "PubChem Source Information". The PubChem Project. USA: National Center for Biotechnology Information. http://pubchem.ncbi.nlm.nih.gov/sources/sources.cgi.
  3. ↑ "all[filt] - PubChem Compound Results". The PubChem Project. USA: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/sites/entrez?term=all%5Bfilt%5D&cmd=search&db=pccompound. Retrieved 7 January 2011.
  4. ↑ "all[filt] - PubChem Substance Results". The PubChem Project. USA: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/sites/entrez?term=all%5Bfilt%5D&cmd=search&db=pcsubstance. Retrieved 7 January 2011.
  5. ↑ "all[filt] - PubChem BioAssay Results". The PubChem Project. USA: National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov/sites/entrez?term=all%5Bfilt%5D&cmd=search&db=pcassay. Retrieved 7 January 2011.
  6. ↑ Script error

External links

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