Structure searching types

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 ... 

OPTION SUBSSS 4 DOING SUB STRUCTURE SEARCH TYPE E TO EXIT... 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

Current chemical information systems offer three principal types of search facility. Structure search involves the search of a file of compounds for the presence or absence of a specified query compound, for example, to retrieve physicochemical data associated with a particular substance. Substructure search involves the search of a file of compounds for all molecules containing some specified query substructure of interest. Finally, similarity search involves the search of a file of compounds for those molecules that are most similar to an input query molecule, using some quantitative definition of structural similarity. 

Answers from all of these searches contain CAS Registry Numbers. Answer sets may be combined, using the Boolean operators AND, OR, or NOT, with other answer sets or with text terms, such as names or molecular formulas. Any answer set also may be used to define subsets of the file for subsequent structure searching. Answer sets of up to 10,000 Registry Numbers from any type of search in this file may also be used as search terms in other files, such as the CA or CAOLD files (53). 

The simplest type of structure search is the identity, or exact match, search. Testing a pair of explicit structures for identity is a problem that has been solved, and for which efficient algorithms now exist [4]. Even between explicit structures, identity comparison can become complicated when issues such as tautomerism, oligomerization, and idiomatic differences in representation (Fig. 5) are considered. 

Because most pharmaceutical, agrochemical, and naturally occurring pyrazines are in fact oxypyrazines of one sort or another,12181281 an alphabetical list of many such recently mentioned pyrazines (under their trivial names, if any) is presented at this point. Each entry includes a chemical name or indication of structure, the type of bioactivity and/or natural source (as appropriate), and the CAS Registrary number and/or leading reference(s) (to facilitate any search for detailed information). 

The EPO esp cenet (ep.espacenet.com) database contains more than 60 million patents from 85 conntries worldwide (not just European Convention countries). The database is searchable by application number, assignee, inventor, or keywords from the title or abstract. Chemical structure searches are not possible. Patents can be viewed as images of the original document in PDF format one page at a time, or the whole patent can be viewed as a text document. Instantaneous translation from French or German into English is available for the latter document type if required. Equivalent pnblished patents, if any, are also listed and are available in PDF format. The text documents do not show chemical structures or diagrams, but these can be viewed in PDF format if required. 

To support the workflow just described, a number of structure and reaction search types have come into use (Fig. 9.11). These are briefly described as follows. 

Exact Match Search. One type of structure searching in which a query molecule is searched for in a database of structures. To exactly match the query, the target structure must be topologically identical and not be a substructure or superstructure of the query. 

Flexmatch Search. Term used in MDL structure searching to allow "relaxed" exact match searching of structures. One can specify, for instance, that everything must match except bond orders, or stereochemistry, or valence at atom centers, etc. By turning on or off various flags, one can for a given structure query, retrieve isomers of various types, salts of a the structure, or instances of the structure that may contain different values of certain types of attached data. 

Similarity Search. A type of "fuzzy" structure searching in which molecules are compared with respect to the degree of overlap they share in terms of topological and/or physicochemical properties. Topological descriptors usually consist of substructure keys or fingerprints, in which case a similarity coefficient like the Tanimoto coefficient is computed. In the case of calculated properties, a simple correlation coefficient may be used. The similarity coefficient used in a similarity search can also be used in various types of cluster analysis to group similar structures. 

Santora, N. J., Auyang, K. Non-computer approach to structure-activity study. An expanded Eibonacci search applied to structurally diverse types of compounds. J. Med. ChettL 1975,18, 959-963. 

Attachments Any type of file information that can be attached to a section similar to e-mail attachments. Examples are texts in a generic format, chemical structures, spectra, chromatograms, and images. These attachments should be searchable using the appropriate search functionality, such as full-text search, structure search, or spectrum. 

Instead of applying additional filtering mechanisms on a hit list, one can evaluate the quality of the pharmacophores to be used as 3D search queries beforehand. The assessment of the quality of a 3D pharmacophore will strictly depend on the main objective(s) of the project (coverage and/or selectivity and/or enrichment). To evaluate one or multiple pharmacophores, one requires a test database that contains i) multiple families of molecules (diverse in structure and type of activity) and ii) a clear activity annotation (if possible with the molecular mechanism of action). Giiner and Henry [44] have developed a series of indices that can be calculated for multiple pharmacophores in order to make an informed decision about the one to be used to screen a virtual library or a corporate collection. 

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. 

We thank Ms. Jan Goranson for skillful typing of the manuscript, Ms. Jean Wisner for thorough proofreading, and Dr. Paul Swepston for assistance with the structural search. JAI thanks the Sherman Fairchild Distinguished Scholars Program of the California Institute of Technology under whose auspices a portion of this review was written. 

In a manner reminiscent of the self-organising maps, the methodology has been applied to produce a subset of the database that represents the best representative of each unique crystal stracture [53]. Thus, a compound with 10 CSD entries, comprising one polymorph determined seven times and a second polymorph determined three times will be reduced to two entries, which are considered to represent the two unique structure types. The details of the applied quality tests are extensive [53], but the result is a list of 231918 structures (derived from 353 666 structures in the November 2005 release) that are considered to be the best representative examples of all unique high-quality stmctures in the CSD [54], In this way, the complete contents of the CSD are reduced to a set of representative structures that contain an equivalent amount of structural information, but without any redundancy. This dataset forms an especially convenient basis for structural searches, since it is free of any duplication. 

Structural (topological) Databases The structural databases play a central role in chemistiy because they contain information on chemical stmctures. Examples of this type are CAS registry, National Cancer Institute (NCI) database, Crystallographic Stracture Database (ICSD), CSD, Protein Data Bank (PDB), etc. The structure databases are usually designed to store chemical stmctinal information representing the chemical bonds and atoms in such a way to use them for computational operations, such as structure search, data mining, etc. 

The simple electronic structure of sodium also renders the application of other types of models relatively easy and extendable to relatively large sizes. See e.g. Hiickel calculations and MC structural search (R. Poteau and F. Spiegelmann, Phys. Rev. B 45, 1878 (1992) and J. Chem. Phys. 98, 6540 (1993) Erratum 99, 10089 (1993)) or the so-called spherically averaged pseudopotential (SAPS) model (M. D. Glossman, J. A. Alonso and M. P. Iniguez, Phys. Rev. B 47, 4747 (1993)). This is a simplified atomistic scheme, in which the external potential (written as the sum of the atomic pseudopotentials) acting on the electrons is developed in spherical harmonics around the cluster center of mass, and only the spherical component is retained in the solution of the KS equations. 

To perform a polymer structure search using ISIS, the searcher uses ISIS/Draw to draw the desired structure, eg, a complete polymer or a fragment. Polymer structure queries may include any of the standard ISIS query properties, eg, atom lists, ring counts, substitution coimts, or bond types. The searcher transfers the drawn structure to ISIS /Base and initiates a search. Search modes... 

EPCs are identified using structured search schemes regarding plant conditions and rules and error types. 

Support software must be developed in each of these areas and integrated into the DBMS for every new abstract data t3q>e. For example, to create a chemical structure ADT, a storage format, such as a connection table format, must first be defined. Then operators for full structure, substructure, and other types ol structure searches must be defined. Access methods need to be implemented to provide fast structure searches and finally, the characteristics of the various structure searches must be made known to the query optimiser to allow efficient overall query execution. 

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