Compound availability databases PubChem

Table 2.2 also lists three publicly available databases commonly used in drug research. PubChem is accessed through the National Library of Medicine (Austin et al., 2004) and contains chemical structure information and corresponding activity across a number of biological assays. The system links the compound information with biomedical literature and it is possible to perform web-based similarity searching. PubChem also enables one to download files with structures to perform chemoinformatic analysis off-line. 

PubChem is organized as three distinct databases PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem Substance contains descriptions of chemical samples, provided by dafa deposifors, and links to information on their biological activities. The description includes PubChem Compound identifiers in cases where the chemical structures of compounds in fhe sample are known. Links providing information on biological activity include those to PubMed [8] citations, protein 3-D structures [9], links to contributor websites, and to biological testing results available in PubChem BioAssay. 

Only recently, initiatives have been started to create freely available data sources such as PubChem,36 ChEBI,37 DrugBank,38 and HMDB,39 to mention some of them. These public databases collect publicly available information on compounds, their structures, their physical formulations (e.g., PubChem Substance), their targets, and their effects on biological processes. However, these databases are far from covering the entire spectrum of chemical information that can be linked to biology and pharmacology. 

The primary eUtil tools of most interest to PubChem users are eSearch, eFetch, ePost, eLink, eHistory, and einfo. eSearch performs an Entrez search, with the same query syntax as web-based Entrez queries (e.g., to query PubChem Compound for the chemical name "aspirin"). eFetch returns an ID list from a prior search (e.g., the list of PubChem Compound identifiers (CIDs) from the aforementioned query of "aspirin"). ePost creates a new ID list by upload of a list of identifiers (e.g., substance identifiers (SIDs)). eLink follows a given link type to create a new ID list from an existing one (e.g., to find all PubChem BioAssay identifiers (AIDs) associated with a list of SIDs). eHistory returns information on current Entrez History entries, einfo lists available Entrez indices and links for a given database. 

PubChem A chemical database is a database specifically designed to store chemical informatioa Chemical stmctures are traditionally represented using hnes indicating chemical bonds between atoms and drawn on paper (2D stmctural formulae). Various chemical databases are available on the Internet which are free for all. Large chemical databases are expected to handle the storage and searching of information on millions of molecules. PubChem is one of the free chemical databases which is developed by the National Center for Biotechnology Information (NCBI). More than 24 millions of compound stmctures and descriptive datasets can be freely downloaded from PubChem. PubChem is a user-friendly database, we can search the compounds by compound name/key word, and we can also search the compound by chemical properties. We can download the compounds in SDF format which is the standard one for various stractural viewers. PubChem has three components, namely PubChem Compounds, PubChem Substances, and PubChem BioAssay described below. 

PubChem Compounds The PubChem Compounds Database contains validated chemical depiction information provided to describe substances in PubChem Substance. Stracmres stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. We can search unique chemical stmctures using names, synonyms, or keywords. Links to available biological properly information are also provided for each compound. 

A number of food phytochemicals and food-related molecular databases are available [21], Food and food-related databases are described in more detail in Chap. 9 of this book. Major examples of public databases of chemical compounds annotated with biological activity for dmg-discoveiy apphcations have been developed. Prominent examples include BindingDB, ChEMBL, PubChem, and WOrld of Molecular BioAcTivity (WOMBAT). These databases and others described in Chap. 9 can be analyzed and compared for knowledge of chemical space coverage and potential repurposing, for example, using the concept of similarity searching. 

Pubchem [32] Pubchem is a database maintained by the National Center for Biotechnology Information (NCBI), which is part of the US National Institutes of Health (NIH). PubChem can be freely accessed through a web user interface or is downloadable by File Transfer Protocol (FTP) at http //pubchem.ncbi.nlm.nih.gov. Pubchem is organized into three main parts substances ( 126 million entries of compound mixtures, extracts, etc.), pure compounds (48 million unique structures), and bioassays (-740,000 records). Users can search the database by name, Pub-Chem identifiers, structures of molecules to retrieve small molecules, calculated physicochemical data, and experimental biological data. Structure-activity relationship tools are available for further analysis of the extracted results. 

National Center for Biotechnology Information PubChem Compound Database CID=3869. Available at http //pub-chem.ncbi.nlm.nih.gov/summary/summary.cgi q=all cid=3869. Accessed 2012 Aug 9. 

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