Getting a list of CIDs for compounds with a given substructure

The input identifiers can also be specified by SMILES or InChI strings, although special care needs to be taken because these identifiers contain special characters (such as “/”) that cause conflicts with the URL syntax.4 

Getting a list of CIDs for compounds identical to a query compound

PUG-SOAP PUG-REST

In PUG-REST, these three pieces of information are encoded into an URL in the following format:

PubChem’s PUG (Power User Gateway), documented elsewhere, is an XML-based interface suitable for low-level programmatic access to PubChem services, wherein data is exchanged through a relatively complex XML schema that is powerful but requires some expertise to use. PUG SOAP contains much of the same functionality, but broken down into simpler functions defined in a WSDL (http://www.w3.org/TR/wsdl), using the SOAP protocol (http://www.w3.org/TR/soap) for information exchange. This WSDL/SOAP layer is most suitable for SOAP-aware GUI workflow applications (Taverna, Pipeline Pilot) and programming languages (C#/.NET, Perl, Python, Java, etc.). See the Tips & Tricks section at the end of this document for more information on specific clients.

heat map-style layout,

the Structure Clustering tool and Structure-Activity Relationship (SAR) Analysis tool.

1.3. Substructure and superstructure search

Lead-like

Components of the rule

MeSH Synonyms

In analogy to the rule of five, it has been proposed that ideal fragments should follow the 'rule of three' (molecular weight < 300, ClogP < 3, the number of hydrogen bond donors and acceptors each should be < 3 and the number of rotatable bonds should be < 3).[1] Since the fragments have relatively low affinity for their targets, they must have high water solubility so that they can be screened at higher concentrations.

Entrez Nodes Are Intended for Linking

The term “data provenance” refers to a record trail that describes the origin or source of a piece of data and the process by which it entered in a database.1 

(d) Explain the reason why the “legacy” designation was introduced in PubChem in two or three sentences.

Some records in PubChem are “non-live”, meaning that they are “not searchable”, although they do exist in the database.  This exercise is designed to help students better understand what non-live records are.

PubChem standardization process in which unique chemical structures are extracted from the Substance database and stored in the Compound database.

Lipinski’sruleof5[50].Among them, 10.3 million (12% of the total) are fragment-like ones, which satisfy Congreve’sruleof3[51].

The PubChem Substance database contains substance information (often including the chemical structure) that was submitted to NCBI by individual submitters (depositors). The PubChem Compound records comprise a non-redundant set of standardized and validated chemical structures. A PubChem Compound record may link to more than one PubChem Substance record if different depositors supplied the same structure. Chemical names shown in PubChem Compound records are a composite derived from all linked substances, with default ranking of names by weighted frequency of use.

JCAMP-DX format

It was recognized in 2004 that there needed to be a successor to JCAMP-DX because of i) advances in technology, ii) a recognized need to represent data from all analytical techniques, and iii) issues with variants of JCAMP-DX that made interoperability of the files difficult.  AnIML files consist of up to four data sections; SampleSet, ExperimentStepSet, AuditTrailEntrySet, and SignatureSet.  By design very little data/metadata is required so that legacy data, which may not have much or any metadata to describe it, can be stored in the AnIML format. An example ‘minimum’ AnIML file is shown below:

widgets

There are currently six InChI layer types, each different class of structural information: the main layer, a charge layer, a stereochemical layer, an isotopic layer, a fixed-H layer and a reconnected layer. 

SMARTS is useful for substructure searching, which finds a particular pattern (subgraph) in a molecule.

aromatic bonds are implied between aromatic atoms, but may be explicitly defined using the ‘:’ symbol.

To make things even more complicated, software may account for the chirality of a stereocenter atom when generating a MOL file but ignore it when rendering a MOL file!

Each of the two Kekulé structures for the benzene ring shows up as a different set of single and double bonds (MOL I, MOL IV). The Bond Tables are different: The MOL file format uses the number 4 to indicate bonds that are explicitly labeled as aromatic (MOL V). This has the advantage of differentiating aromatic bonds from single and double bonds without requiring the chemist to write a script to identify and label the alternating single and double bonds of a Kekulé structure.

The MOL file format uses the number 4 to indicate bonds that are explicitly labeled as aromatic (MOL V). This has the advantage of differentiating aromatic bonds from single and double bonds without requiring the chemist to write a script to identify and label the alternating single and double bonds of a Kekulé structure. However, some software may not be built to handle this convention. (You might even run into cases in which it’s interpreted as a quadruple bond!)

Of course, chemical structuresand topological graphs are not entirely equivalent: aconnection table is akin to a description of a singlevalence bond structure and does not take account,for example, of delocalized bonds.Alternative approaches have been suggested.

n InChI Keycan also be generated for a compound. This is completely separate from the InChI linear notation, and is used to provide an identifier for a compound that is particularly suitable for use in Web search engines. It is an ASCII character string based on a hashing of the InChI linear notation, but is of fixed length and uses only characters not normally conside