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PubChem is a database of chemical molecules. A Computer Database is a structured collection of records or data that is stored in a computer system Chemistry (from Egyptian kēme (chem meaning "earth") is the Science concerned with the composition structure and properties In Chemistry, a molecule is defined as a sufficiently stable electrically neutral group of at least two Atoms in a definite arrangement held together by 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). The National Center for Biotechnology Information ( NCBI) is part of the United States National Library of Medicine (NLM a branch of the National Institutes The United States National Library of Medicine ( NLM) operated by the United States federal government, is the world's largest Medical library. "NIH" redirects here For other meanings of NIH see NIH (disambiguation. PubChem can be accessed for free through a web user interface. The user interface (or Human Computer Interface) is the aggregate of means by which people&mdash the users '&mdash interact with the System 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. The American Chemical Society ( ACS) is a Learned society ( Professional association) based in the United States that supports scientific inquiry The United States Congress is the bicameral Legislature of the federal government of the United States of America, consisting of two houses Chemical Abstracts Service ( CAS) is a division of the American Chemical Society, and produces Chemical Abstracts, and related products [1]. More than 80 database vendors contribute to the growing PubChem database. [2]

Contents

Databases

PubChem consists of three dynamically growing primary databases:

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 is a way of expressing information about the Atoms that constitute a particular Chemical compound, and how the relationship between those atoms changes The molecular mass (abbreviated m of a substance, more commonly referred to as molecular weight and abbreviated as MW, is the Mass of one In the fields of organic and Medicinal chemistry, a partition (P or distribution coefficient (D is A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen

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. A molecule editor is a Computer program for creating and modifying representations of Chemical structures There are a number types of molecule editor The IUPAC International Chemical Identifier ( InChI, pronounced "INchee" is a textual Identifier for Chemical substances designed to provide a

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. PubMed is a free search engine for accessing the MEDLINE database of citations and abstracts of biomedical research articles

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. Table of logic symbolsIn Logic, two sentences (either in a formal language or a natural language may be joined by means of a logical connective to form a compound sentence 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]

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. Lipinski's Rule of Five is a Rule of thumb to evaluate Druglikeness, or determine if a Chemical compound with a certain pharmacological or The American Chemical Society ( ACS) is a Learned society ( Professional association) based in the United States that supports scientific inquiry Chemical Abstracts Service ( CAS) is a division of the American Chemical Society, and produces Chemical Abstracts, and related products 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. '

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]

See also

External links

Medical Subject Headings ( MeSH) is a huge Controlled vocabulary (or metadata system for the purpose of indexing journal articles and books IUPAC Nomenclature is a system of naming Chemical compounds and of describing the science of Chemistry in general The IUPAC International Chemical Identifier ( InChI, pronounced "INchee" is a textual Identifier for Chemical substances designed to provide a The molecular mass (abbreviated m of a substance, more commonly referred to as molecular weight and abbreviated as MW, is the Mass of one A chemical element is a type of Atom that is distinguished by its Atomic number; that is by the number of Protons in its nucleus. Isotopes (Greek isos = "equal" tópos = "site place" are any of the different types of atoms ( Nuclides Chemistry, a formal charge (FC is a Partial charge on an Atom in a Molecule assigned by assuming that Electrons in a Chemical The term chiral (pronounced /ˈkaɪɹ(əl̩/ is used to describe an object that is non- superimposable on its mirror image A hydrogen bond results from a Dipole-dipole force between an Electronegative atom and a Hydrogen atom bonded to Nitrogen, Oxygen Tautomers are Organic compounds that are interconvertible by a Chemical reaction called tautomerization. In the fields of organic and Medicinal chemistry, a partition (P or distribution coefficient (D is A chemical database is a Database specifically designed to store chemical information. Chemspider is a chemical Database. The system was first launched in March 2007 in a beta release form and transitioned to release in March 2008 eMolecules is a Search engine for chemical Molecules The system was first launched in November 2005 The DrugBank database available at the University of Alberta is a unique Bioinformatics and Cheminformatics resource that combines detailed drug (i Moltable is a Drug research initiative based in India, aimed at discovering new drugs to target Cancer, AIDS, Malaria and other potentially The National Center for Biotechnology Information ( NCBI) is part of the United States National Library of Medicine (NLM a branch of the National Institutes The Entrez Global Query Cross-Database Search System is a powerful Federated search engine or Web portal that allows users to search many discrete Health sciences PubMed is a free search engine for accessing the MEDLINE database of citations and abstracts of biomedical research articles The GenBank Sequence database is an Open access, annotated collection of all publicly available Nucleotide sequences and their Protein translations
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