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 mostly small molecules with a molecular mass below 2000 u. 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 50 database vendors contribute to the growing PubChem database.[2] Image File history File links Pubchemlogo. ... The term or expression database originated within the computer industry. ... Chemistry (from Persian language کیمیا Kimia and Greek χημεία khēmeía[1] meaning alchemy) is the science of matter at the atomic to molecular scale, dealing primarily with collections of atoms, such as gases, molecules, crystals, and metals. ... In chemistry, a molecule is an aggregate of two or more atoms in a definite arrangement held together by chemical bonds [1] [2] [3] [4] [5]. Chemical substances are not infinitely divisible into smaller fractions of the same substance: a molecule is generally considered the smallest particle of a pure... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The U.S. National Library of Medicine (NLM), operated by the U.S. federal government, is the worlds largest medical research library. ... The National Institutes of Health (NIH) is the primary agency of the United States government responsible for medical research. ... The user interface is the aggregate of means by which people (the users) interact with a particular machine, device, computer program or other complex tool (the system). ... The molecular mass (abbreviated MM) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12). ... The unified atomic mass unit (u), or Dalton (Da), is a small unit of mass used to express atomic and molecular masses. ... The American Chemical Society (ACS) is a learned society (professional association) based in the United States that supports scientific inquiry in the field of chemistry. ... Congress in Joint Session. ... Chemical Abstracts Service (CAS) is a division of the American Chemical Society, and produces Chemical Abstracts, and related products. ...

Databases

PubChem consists of three dynamically growing primary databases:

• Compounds, 10.1 million entries, contains pure and characterized chemical compounds. Check the accurate number of compounds online.[3]
• Substances, 15.5 million entries, contains also mixtures, extracts, complexes and uncharacterized substances. Check accurate number of substances online.[4]
• BioAssay, bioactivity results from 337 high throughput screening programs with several million values. Check accurate number of bioassays online.[5]

An extract consists of a certain percentage of true essence, or its chemical imitation, in an alcoholic solution. ... Synthesis of copper(II)-tetraphenylporphine, a metal complex, from tetraphenylporphine and copper(II) acetate monohydrate. ... Bioactivity refers to the effect of a given agent, such as a vaccine, upon a living organism or on living tissue. ... High-throughput screening, often abbreviated as HTS, is a method for scientific experimentation especially relevant to the fields of biology and chemistry. ...

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. A chemical formula (also called molecular formula) is a concise way of expressing information about the atoms that constitute a particular chemical compound. ... The molecular mass (abbreviated MM) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12). ... A partition coefficient or distribution coefficient is a measure of differential solubility of a compound in two solvents. ... Snapshot from a simulation of liquid water. ...

PubChem contains an 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. A molecule editor is a computer program for drawing and editing chemical structures. ... The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. ... The IUPAC International Chemical Identifier (InChI), developed by IUPAC and NIST, is a digital equivalent of the IUPAC name for any particular covalent compound. ...

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. Medline is a comprehensive literature database of life sciences and biomedical information. ...

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. In logical calculus, logical operators or logical connectors serve to connect statements into more complicated compound statements. ...

Example (Lipinski's Rule of Five): In 1997 Christopher A. Lipinski published a seminal paper identifying a series of features commonly found in orally active drugs. ...

 0:500[mw] 0:5[hbdc] 0:10[hbac] -5:5[logp] 

Database fields

Medical Subject Headings (MeSH) is a huge controlled vocabulary (or metadata system) for the purpose of indexing journal articles and books in the life sciences. ... IUPAC nomenclature is a systematic way of naming organic chemical compounds. ... The IUPAC International Chemical Identifier (InChI), developed by IUPAC and NIST, is a digital equivalent of the IUPAC name for any particular covalent compound. ... The molecular mass (abbreviated MM) of a substance, formerly also called molecular weight and abbreviated as MW, is the mass of one molecule of that substance, relative to the unified atomic mass unit u (equal to 1/12 the mass of one atom of carbon-12). ... The periodic table of the chemical elements (this version outdated on October 13, 2006) A chemical element, or element for short, is a pure substance that cannot be decomposed into any simpler substance. ... Isotopes are any of the several different forms of an element each having different atomic mass. ... In chemistry, a formal charge (FC) on an atom in a molecule is defined as: FC = number of valence electrons of the atom - number of Lone pair electrons on this atom - half the total number of electrons participating in covalent bonds with this atom. ... The term chiral (pronounced ) is used to describe an object which is non-superimposable on its mirror image. ... Snapshot from a simulation of liquid water. ... Tautomers are organic compounds that are interconvertible by a chemical reaction called tautomerization. ... A partition coefficient or distribution coefficient is a measure of differential solubility of a compound in two solvents. ...

See also

• Chemical database
  • eMolecules
  • DrugBank
• National Center for Biotechnology Information (NCBI)
• Entrez
• PubMed
• GenBank
• Chemistry resources

To meet Wikipedias content policies, the external links section for this article may require cleanup. ... eMolecules is a database of chemical molecules. ... The DrugBank database available at the University of Alberta is a unique bioinformatics and cheminformatics resource that combines detailed drug (i. ... The National Center for Biotechnology Information (NCBI) is part of the US National Library of Medicine (NLM), which is a branch of the US National Institutes of Health. ... The Entrez logo The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Medline is a comprehensive literature database of life sciences and biomedical information. ... The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. ...

External links

• PubChem homepage
• PubChem searchpage
• PubChem FAQ
• PubChem Help