Pubchem database

Descriptors used to characterize molecules in QSAR studies should be as independent of each other (orthogonal) as possible. When using correlated parameters there is an increased danger of obtaining non-predictive, chance correlation [56]. To examine the correlation between PSA (calculated according to the fragment-based protocol [10]) and other descriptors, we studied a collection of 7010 bioactive molecules from the PubChem database [57]. In addition to PSA, the following parameters were used ... 

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... 

NIH Molecular Libraries Roadmap Initiative and the PubChem Database... 

The PubChem database contains more than 10 M chemical structures and is publicly available on the web (http //pubchem.ncbi.nlm.nih.gov)... 

Other properties are not unique, for example, chemical names. These should be stored in a separate table with one row for each value. For example, the entry in the pubchem database contains 10 synonyms for the SMILES C1(C(C(C(C(C10)0)0P(=0)(0)0)0)0)0 as shown in Table 13.1. Each of these should be entered as a separate row in a table of names along with a column containing the compound id. A simple table of this type would be created using the following SQL. 

The fundamental relationships between the three PubChem databases are straightforward. PubChem Substance identifiers (SIDs) relate to PubChem Compound... 

A critical concept for the advanced PubChem user is that of combining and transforming sets of identifiers between the three PubChem databases, based on the above identifier relationships. For instance, there is a many-to-one relationship between SIDs and "standardized" CID, as more than one Substance depositor may have supplied the chemical structure that standardizes to a given CID. (In fact, even within a particular depositor s records, there may be redundant structures because of different sample origins, tautomeric forms, etc.). Also, the perceptive reader will notice there is not a direct relationship between Bio Assay (AID) and Compound (CID) identifiers. To discover assays linked to a CID, there is an expansion of that CID to all SIDs for which that CID is the standardized form AIDs can be associated with CIDs linked to any of these SIDs. 

PubChem databases have a number of additional controls that operate on a query result list, such as icon buttons (provided after Tools") for assay data analysis and chemical structure download. There are pop-up link menus (provided after "Links" on the same line as "Tools") that provide powerful query result list operations. Also, the pop-up link menus exist for each record, but they function only on the individual record. The meaning of these links is detailed further in the following sections. 

Knowing what indices are available in a database is the key to maximizing the power of an Entrez search. The indices may be listed by going to the "Preview/Index" tab in Entrez, and opening the menu on the bottom left. Also, this page provides an interface for constructing index-specific queries. A complete list and description of the Entrez indices available for the three PubChem databases are detailed in the "Indices and Filters in Entrez" section of the help documentation (http // pubchem.ncbi.nlm.nih.gov/help.html). 

Filters are related to links in that the majority of filters in the PubChem databases are generated automatically based on the presence of links. In the above example the "pcsubstance pcassay" filter has a "true" bit for every substance for which a PubChem BioAssay link is present (e.g., in the pop-up menus of the Entrez DocSum for that substance). 

We have described how PubChem databases are integrated into Entrez, enabling detailed and flexible searches across the PubChem data however, Entrez is essentially a text search engine and is not amenable to more detailed chemical and bioassay data analysis. Such analysis must be handled by specialized applications. 

Chemistry is one of the first scientific disciphnes that employed databases to store the chemical informatioa There are a wide variety of chemical databases available in chemistiy. Here, we describe the list of available chemical databases which are very nsefiil and freqnently nsed for computational modelling and chemoinformat-ics activities. Recently, National Institute of Health (NIH) took initiatives to collect molecular stractures from publicly available resources and oiganized them in a single database called PubChem Database containing over 30 millions of unique molecular entries and made it available for free to the public [93], Due to the huge and continuously increasing amount of data related to chemical information, it is... 

Cincilla, G., Thormarm, M., and Pons, M. (2010) Structuring chemical space similarity-based characterization of the PubChem database. Molecular Informatics, 29, 37 9. 

The PubChem Dataset A randomly selected subset of 1000 measured solubility values selected from a set of 58,000 values that were experimentally determined using chemilumenescent nitrogen detection (CLND) by the Sanford-Bumham Medical Research histimte and deposited in the PubChem database (AID 1996) [23] This dataset is composed primarily of screening compounds from the NIH Molecular Libraries initiative and can be considered representative of the types of compounds typically found in early stage drug discovery programs. Values in this dataset were reported with a qualifier < to indicate whether the values were below,... 

The METLIN metabolite database is implemented using the open-source software tool, MySQL. Most compounds are annotated with both a chemical formula and structure. Individual metabolite is linked to outside resources such as the KEGG, Human Metabolome Database (HMDB), and the respective PubChem database entries through the included numbers of KEGG, HMDB, and Chemical Abstract Service (CAS), respectively. This kind of linkage makes it easy for the researchers to find further references and inquiries about the metabolite. 

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