PubChem Structure Search

Find chemical structures of small organic molecules and information on their biological activities in the three new Entrez PubChem databases Compound, Substance, and SioAssay. Try PubChem Structure Search" to query the databases with a structure. More... 

The PubChem structure search tool enables one to query and subset PubChem Compound by a variety of chemical structure search types and optional filters. The chemical structure search service may be directly accessed using the URL ... 

Xx Pubchem Compound Search unique chemical structures using names. 

Structure Search Search PubChem s Compound database using a chemical structure as the query, structures may be sketched or specified by SMILES, MOL hies, or other formats. 

PubChem Chemical Structure Search South SMUS or Fornmfe [d-CC-CC-Cl Shofcli... 

The enormous databases compiled by organizations such as PubChem (Ref 4), the U.S. National Cancer Institute (NCI), and ChemSpider (Ref 5) contain millions of InChls and InChIKeys, which allow sophisticated searching of these collections. PubChem provides InChl-based structure-search facilities for both identical and similar structures (Ref 6), and ChemSpider offers both search facilities and Web services enabling a variety of InChl and InChIKey conversions (Ref 7). The NCI Chemical Structure Lookup Service (Ref 8) provides InChl-based search access to over 39 million chemical structures from over 80 different public and commercial data sources. 

PubChem archives the molecular structure and bioassay data from the MLSCN and other contributors. PubChem provides search, retrieval, and data analysis tools to optimize the utility of these results. PubChem further enhances the research utility of the MLSCN output by including other public sources of chemical structure and bioactivity information and by integration of this data with other NIH biomedical knowledgebases. The primary aim of PubChem is to provide a public on-line resource of comprehensive information on the biological activities of small molecules accessible to molecular biologists as well as computational and medicinal chemists. 

The supported query input formats for fhe structure search tool are SMILES, SMARTS [17], InChl, CID (PubChem Compound identifier), molecular formula, and SDF [18]. There is also an online JavaScript-based chemical structure sketcher through which a query may be manually drawn, edited, or imported. The sketcher is compatible with modem web browsers and does not require special software to be downloaded or installed. 

While the input query and search type are all that are necessary to perform a sfmcfure search in PubChem, there are numerous choices by which one may narrow the search to smaller subsets of PubChem. For example, one may search only within a previous Entrez search result, or even a previous stmcture search result, or upload a file of ClDs againsf which fhe search is fo be performed. One may filter based on a wide variety of properties, such as molecular weight, heavy atom count, presence or absence of stereochemistry, assay activity, elemental composition, depositor name or category, etc. Most of these subset operations could be accomplished through appropriate Entrez index queries followed by Boolean operations on structure search results however, the structure search tool provides a convenient one-step interface for chemical search refinement. 

This service takes as input a chemical structure and (if sfandardization is possible) oufputs a chemical sfrucfure. Allowed sfructural inpuf and output formats include SMILES, InChl, or SDF file however, fhe input and output formats need not be the same. As with structure search, the standardization service is queued on PubChem servers, meaning a request may not start right away or may not complete immediately. One may also import and export standardization requests to a local XML file to serve as an example for consfrucfing queries for the PUG interface (described in detail later). 

PubChem tools for structure search, standardization, and downloads are enabled via PUG, with more to be added. In each case, the options available through PUG are the same as those available through the interactive web pages, including all the advanced options and filters of the structure search service. In fact, most of the web tools can write out queries in PUG s XML format, which can be sent directly to PUG or used as templates for constructing new PUG requests. 

Human Protein Reference Database http //www.hprd.org/protein PubChem - Chemical structures of small organic molecules and information on their biological activities http //pubchem.ncbi.nlm.nih.gov Search within the archive of websites http //www.archive.org... 

PubChem is organized as three linked databases within the NC8I s Entrez information retrieval system. These are PubChem Substance. PubChem Compound, and PubChem BioAssay. Pubchem also provides a fast chemical structure similarity search tool. More information about using each component database may be found using the links above. 

Finally, we will identify the structure of enriched ions by using accurate mass (obtained during our standard MS experiments) and searching metabolite databases, such as METLIN [75], PubChem [76], or the lipid MAPS [77] for... 

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. 

In order to find structures and data in PubChem, there are search tools available online.2 This may suffice for your needs. The data are also available in the form of SDF files and csv (comma-separated values) files. 

Today, I have turned my habit around. When I have a set of chemical structures or data files, my first task is to organize them in a relational database. After all, the tools I now use are designed to read and write tables in a database. Rather than creating folders to keep project files, I create a schema of tables with rows holding chemical structures and data imported from the files. For example, the PubChem project provides information on millions of compounds in the form of hundreds of chemical structure files and associated experimental data files. While PubChem provides excellent Web tools to search this data, for local use I developed a schema to hold the structures and data in related tables. One possible schema for this is shown in Chapter 6 of this book. 

PubChem Compound contains the unique chemical structure content of PubChem Substance. Compounds may be searched by computed chemical properties and are pre-clustered by structure comparison into identity and similarity groups. Whenever possible, compounds are linked via PubChem Substance to information on their biological activities. 

By default, when one enters a simple query in the Entrez search interface, that query is matched against all indices in that database. For example, if one searches "aspirin" in PubChem Compound, Entrez will report back any records with an index that contain "aspirin" as (any word in) a synonym, a depositor comment, etc. This is why a text search for "aspirin" also currently brings up the structure of acetaminophen, considering one of the names supplied by a depositor for acetaminophen is "Aspirin-Free Anacin," and so an unrestricted search for "aspirin" will match this record, as well. 

Multiple indices may be searched simultaneously using Entrez s Boolean operators. For example, a query in PubChem Compound of "Br[Element] AND l[CovalentUnitCount]" will find all chemical structures containing the element bromine and that are not part of a mixture. Please note that Entrez Boolean operators are capitalized (e.g., "AND," "OR," and "NOT"). 

Entrez history is used heavily by PubChem tools (which are not a part of Entrez) so results of user searches can be used as a subset for further manipulation. Eor example, the chemical structure download service (described below) reads Entrez history items, so one can generate an SDF file containing just those compounds found in a PubChem Compound Entrez result set. For example, the BioAssay tools (also described below) make frequent use of Entrez history, so that structure queries can be used to subset assay results in a chemical structure analog series. 

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