Markush structures – From molecules towards patents 2009 ICIC presentationPresentation by Szabolcs Csepregi, Nóra Máté, Róbert Wagner, Szilárd Dóránt, Erika Biró, Tamás Csizmadia, Tim Dudgeon, Ferenc Csizmadia · October 2009
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent applications for the description of compound classes.
Full abstractThe presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and larger repeating units, position and homology variation). It will be shown how Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space searched without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).
The presentation will focus on the most recent developments (position variation, repeating units, homology variation), and further developments will be discussed towards full patent handling.
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Representation, searching & enumeration of Markush structures - from molecules towards patents - 2009 updatePresentation by Erika Biró, Ferenc Csizmadia, Nóra Máté, Róbert Wagner, Szabolcs Csepregi, Szilárd Dóránt, Tamás Csizmadia · August 2009
Cheminformatics systems usually focus primarily on handling specific molecules and reactions. However, Markush structures are also indispensable in various areas, like combinatorial library design or chemical patent applications for the description of compound classes.
Full abstractThe presentation will discuss how an existing molecule drawing tool (Marvin) and chemical database engine (JChem Base/Cartridge) are extended to handle generic features (R-group definitions, atom and bond lists, link nodes and larger repeating units, position and homology variation). It will be shown how Markush structures can be drawn and visualized in the Marvin sketcher and viewer, registered in JChem databases and their library space searched without the enumeration of library members. Different enumeration methods allow the analysis of Markush structures and libraries. These methods include full, partial and random enumerations as well as calculation of the library size. Furthermore, unique visualization techniques will be demonstrated on real-life examples that illustrate the relationship between Markush structures and the chemical structures contained in their libraries (involving substructures and enumerated structures).
The presentation will focus on the most recent developments (position variation, repeating units, homology variation), and further developments will be discussed towards full patent handling.
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Instant JChemPresentation by Tim Dudgeon · March 2009
Instant JChem is ChemAxon’s desktop chemistry solution, allowing scientists to manage and search chemical structures and related information. This presentation gives an overview about the most important features of the Instant JChem, it describes the typical users of the tool and gives an idea about the upcoming developments for short and medium terms.
Full abstract The description of the Instant JChem is built around ten bullet points:
- Simple and flexible deployment
- Create and manage structure databases
- Import/export/merge/edit data
- Build tabular and form based reports
- Run combined structure and data searches
- Structure based predictions
- Manage relational data
- Access sophisticated chemistry features
- Collaborate with other users
- Extensible
Among the most typical usage scenarios of the Instant JChem the building of the database is fundamental. Afterwards customers usually use the Instant JChem to create reports from the existing database, share data and customize the tool to fulfill their own needs. The future development of the product contains mostly the synchronization with other JChem releases. It means that the next release of the Instant JChem will improve the database’s server, the schema editor, the handling of the URL fields and probably the Reactor will be integrated to it.
2009 Instant JChem Seminar Series · Feb-March 2009
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Markush search and enumerationMarch 2009
The Markush structures describe a compound class by generic notation through R-groups, atom or bond lists, repeating units, position or homology variation, etc. and so they are feasible to define the patent claims and combinatorial libraries. The ChemAxon’s Markush project aims to extend structural search capabilities and enable the Markush enumeration.
Full abstractThe first part of the presentation gives an overview of the existing Markush functionalities, like the features of the combinatorial Markush structure handling, the existing enumeration methods and the Markush structure reduction. The Markush features are implemented as Markush database tables in two chemical databases of the ChemAxon, in the JChem Base and in the Instant JChem. Among the 2009 improvements worth to mention the repeating unit with repetition ranges, the homology groups and the identification of R-group definitions from reagent files.
Regarding the future the ChemAxon’s Markush development plans are related mostly to the patent claims.
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Working with IUPAC names using ChemAxon toolsPresentation by Daniel Bonniot de Ruisselet, Veréb Rita, Miklós Vargyas · August 2008
Chemical names constitute a widely used and convenient way to characterize compounds. Historically, useful compounds have been assigned common names, like toluene. Systematic ways to assign names to all compounds have later been developed and standardized by the International Union of Pure andApplied Chemistry (IUPAC).
Full abstractSuch systematic names reveal the presence of characteristic groups, like carboxylic acids and classes of compounds, like esters. Currently, IUPAC is designing precise rules to assign a unique preferred name to each compound, which can be useful, for instance, in the context of patents.
ChemAxon provides tools to generate names from structures, and to generate structures from names. In both cases, we strive to support both traditional and preferred IUPACnames.
236th ACS National Meeting & Exposition · August 17-21, 2008
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