Exact structure search

Similarity is very subjective, as it depends on what are we looking for and from what point of view we are looking. For example, from a mathematical point of view, we would denote two molecules as similar if they have common features in three dimensions, whereas if we take a chemical approach, we would denote two molecules as similar if they had similar physical properties. Similarity-based methods have gained popularity due to the rapid technological progress and increased number of entries in chemical databases. This has made the application of computational search methods a necessity. 

Similarity measures are generally based on the presence and/or absenee of features in two molecules. Similarity can be measured by numerieal or distance mea-smes. The former involves the expression of similarity by a numerieal value in the range of 0-1, while the latter involves the expression of similarity in numerieal value not less than 0. These measures are discussed in detail later in the chapter. In the next sections of this chapter, you will come to know about the various similarity-searching techniques and similarity matrices. 

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A structure search of chemical substances can be performed in the chemical structure databases. The structure query can be input using a graphical structure editor. The following search methods are possible, depending on the type of structure database. The structure search capabilities depend on the software system. Here, the focus is on the implementation of STN International exact structure search, family search, substructure search, similarity search, generic (Markush) search, and reaction search. 

Exact structure searching involves the retrieval of all entities in a CIR system that match exactly and completely... 

During an Exact Structure Search (EXA) (Sect. 7.2.4) only those substances which exactly match the query are searched, additional substituents are disregarded (Fig. 99). Multicomponent substances or salts are excluded. The query s result may consist of more than one piece of information, because all stereo isomers or isotope compounds, for example, match the search profile exactly. 

Like the Exact Structure Search, Family Searches (FAM) also do not allow further substitutions. The result consists of compounds that match exactly the request, and also of multicomponent substances as well as salts, such as the potassium salt of piceol in Fig. 100. 

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. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

Before finally storing the structure in the database, the registration program may search the database for some level of match to the input structure or reaction, and skip the registration if it is a duplicate. This is sometimes termed "deduplication" through "exact match" searching. There is usually some redundancy in chemical databases, and to save search time and disk space, most companies do not store duplicate structures or reactions, but rather store pointers to them. 

Exact Match Searching. Here, the chemist has a particular structure (or reaction) that he wishes to find in the database. The structure/reaction is drawn using a drawing program and then passed to a search program. The program submits the query to the... 

Deduplication. When registering into a chemical structure database, the process of finding whether the given structure already exists in the database. This usually involves performing an exact match search with the given structure as the search query. Note that the definition of exact match may vary with the database, and it may even be configurable. For example, some databases may consider tautomers to be acceptable as exact matches, whereas others may require a more strict definition. 

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. 

The chemicals stored in the inventory can be searched by exact structure, substructure, or similarity [26], Similarity searching aims at retrieving compounds that are similar to a query compound by one or more measures of similarity. A set of structural features of the target molecule is compared with those of each chemical in the database, generating a similarity measure by a chosen metric such as the Tanimoto coefficient [27]. More details about chemical similarity are given below in relation to the chemical similarity tool. 

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