PubChem

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PubChem is a database of chemical molecules. 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]

Contents

[edit] Databases

PubChem consists of three dynamically growing primary databases:

  • Compounds, 18.4 million entries, contains pure and characterized chemical compounds. Check the accurate number of compounds online.[3]
  • Substances, 38.6 million entries, contains also mixtures, extracts, complexes and uncharacterized substances. Check accurate number of substances online.[4]
  • BioAssay, bioactivity results from 598 high-throughput screening programs with several million values. Check accurate number of bioassays online.[5]

[edit] 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]

[edit] American Chemical Society Concerns with PubChem

The American Chemical Society has raised serious 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. They are reported to have paid the lobbying firm Hicks Partners LLC at least $100,000 in 2005 to try to persuade congressional members, the NIH, and the Office of Management and Budget (OMB) against establishing a publicly funded database. They also were reported to have spent $180,000 to hire Wexler & Walker Public Policy Associates to promote the 'use of [a] commercial database.'

[edit] Database fields


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]

[edit] See also

[edit] External links