Searching Markush

ChemAxon Ltd. Markush Search and Enumeration, http //www.chemaxon.com/products/ markush-ip/. Accessed 2013 May 14. 

Under Substances, search options include chemical structures, molecular formulas, and properties. Chemical structures may be searched as exact matches, substructures, and similarity matches. Exact matches will include enantiomers, stereoisomers, radicals, salts, and the like. These results can be filtered once the search is complete. Substructure matches allow substitution at any positions not specifically blocked. A similarity search is the broadest category. If an exact search doesn t result in sufficient matches, a substructure search may yield results. Markush searching is also available. Markush structures are found in the patent... 

MARPAT. The MARPAT File is a Markush search service (see Markush Structure Searching in Patents). It contains the Markush structure records for patents found in the CA File with patent publication year 1988 to the present. The records contain the Markush structures found in the claims and often the disclosure of the patent, the bibliographic information, in-depth substance and subject indexing including CAS Registry Numbers, and an abstract, all of which are displayable. The structures are structure-searchable. CAS roles... 

At this juncture, Markush search systems for patents are fairly mature. The fragment code and graphical systems in... 

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. 

Markush searches are generic substructure searches. It should be clear that both structure queries and structure files may contain specific and/or generic Structures. In a Markush search generic chemical structures are searched against a database which contains specific or generic structures. The first type of database is a registry file, e.g., the CAS REGISTRY, and the second type is a Markush file, e.g., MaRPAT (see Structure Representation). 

In the case of the second problem, however, it is both possible and desirable to give a definition of the search tool, and that is the purpose of this paper. The LN is a flexible and useful tool, but contains the seeds of much difficulty if the concept is applied incautiously. It is not a type of substructure searching, nor is it a Markush search. To repeat the above objective once more, the intention behind the LN is to retrieve those sorts of structures which one might have found within a few pages of the given structure, had the user been looking in an Omnibus Edition of the Beilstein Handbook. 

Nowadays, Markush structures are utilixed mainly in patent databases, where they describe a number of different chemical compounds. Searching in patent databases is very important for companies to ascertain whether a new compound is... 

Today, fragment coding is still quite important in patent databases (sec Chapter 5, Section 5.11, e.g., Dei went) where Markush structures are also stored. There, the fragments can be applied to substructure or othei types of searches where the fragments arc defined, c.g., on the basis of chemical properties. 

We should not minimize the effects that electronic searching of patents has had on the business of research. In 1990, CAS introduced MARPAT, which is a database of Markush (generic) structures found in patent documents [1]. This database provided a valuable tool for patent searching in a more comprehensive way than had been available previously. In 1995, CAS launched SciFinder, which provided access to the patent literature for chemists on their desktops. Using the SciFinder interface, one may search for research topics, authors, companies, or structures/reactions. From a practical viewpoint, SciFinder did more to enhance the searching capabilities of the medicinal chemist than any other tool. Even today, SciFinder continues to provide a first pass through the patent literature when chemists want to include patents in their searching. Indeed, when a search is performed, patent references are included in the answer set. Only very recently have there been additional tools to search the patent literature that have found widespread use. 

Markovnikov rule, 20 774 Markov property, 26 1022 Markush chemical structures, indexing and searching, 18 242. See also WPI entries... 

This is the standard library design scenario which is supported by most in-house and commercial vendor tools. The user-defined reaction is usually a Markush reaction drawing commonly in the format of MDL ISIS sketch or. rxn file (35). Chemists may also supply reactant sets for each reaction component either by loading pre-defined sets of molecules or by retrieving them via searches into chemical reactant databases. Molecular property calculations and analysis on the reactants are performed, and selections are made based on these results. This is commonly known... 

WPIM (World Patents Index Markush), produced by Derwent Publications, Ltd., contains the specific and generic structure records for compounds in the patents included in Derwent Sections B (Farmdoc), C (Agdoc), and E (Chemdoc) since 1987. Sources include patents from 29 industrialized countries as well as European and PCT patents and also items from Research Disclosure and International Technology Disclosures. The compound numbers of relevant references found in WPIM can be searched in Derwent s WPI database to retrieve the corresponding bibliographic information. 

Let s consider a patent application that contains a claim including the Markush group we have drawn in Figure 7.1. The claim containing the naphthalene Markush is shown in Figure 7.2. A prior art search reveals the following disclosures ... 

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