Structure representation generic

Structure 1 Generic representation of the structures of basic types of binary phosphorus-nitrogen heterocycles cyclophosphazanes (I), cyclophosphazenes (II), cyclic phosphoranes (III)... 

Structure 3 Generic representation of the structures of IV-heterocyclic carbene analogues... 

METEOR S biotransformation rules are generic reaction descriptors, and the versatile structural representation used in the system allows each atom or bond to have specific physicochemical properties. This approach provides more details than simple hard-coded functional group descriptors (313), but this flexibility also can give rise to an avalanche of data. METEOR manages the amount of data by predicting which metabolites are to be formed rather than all the possible outcomes (310,312,314,315). At high certainty levels, when chosen, only the more likely biotransformations are requested. At lower likelihood levels, the more common metabolites are also selected for examination. Currently, METEOR knowledge-based biotransformations are exclusively for mammalian biotransformations (phase I and phase II) (314,315). 

The structural representation of combinatorial chemistry consists of a generic structure plus a list of substituents that may be present in that structure. 

Figure 9.6. Chemical structure data for high-throughput chemistry. The generic structure representation is often referred to as a Markush structure.

Markush structure A type of structure representation in which very general lemis. such us alkyl or alcohol, can be used to describe the substituents in a generic structure. Used in the patent literature and adapted for combinatorial chcmi.slty publications. 

Management is to allow structured representations of data - referred to as models -to be manipulated in bulk by using a set of generic and reusable operators. Because these works concentrate on the schema level rather than the data level, they do not consider instance level constraints. 

For compounds for which X-ray data have not yet been obtained, generic structural representations are shown. For these reagents, traditional nomenclature, such as uronium salts, has arbitrarily been retained. 

Fliri, A., Moysan, E., Benichou, P., and Nolle, M. (2009) Methods for processing generic chemical structure representations. Patent W009051741. 

Generic or Markush structures are a form of structural representation that can be used to encompass many individual molecules having common structural features. Figure 6.5 shows a simple example. They are particularly associated with chemical patents,but may also be used (often with a table of values for the R-groups) to represent sets of related molecules involved in structure - activity relationship studies, or large combinatorial libraries. The RGfile variant of the Molfile format can represent restricted forms of Markush structure, as can Sybyl line notation,and a variety of vendors have implemented ad hoc extensions (which have some Markush capabilities) to SMILES. 

Fisanick, W. Storage and Retrieval of Generic Chemical Structure Representations by Computer. U.S. patent US 4,642,762A, 10 Feb 1987. 

The iterative search algorithm is being completely rewritten for the search engine implementation to support the use of generic search queries against a file of Markush structure representations. That is, both the queries and the structures on a file may have nodes represented as variable substructures or certain generic nodes (e.g., heterocycle). 

Substance information such as chemical structures, molecular formulas, and chemical names Is stored in the REGISTRY database. This is the largest collection of chemical substance Information worldwide (see Section 3,1,2), While REGISTRY contains information on specific substances, generic substances are covered by MARPAT, Generic structures are called Markush structures after the American chemist Eugene Markush, who introduced these structures in the patent literature in 1924, MaRPAT comprises generic structures from the patent literature since 1988 (see Structure Representation). Chemical reactions or molecular transformations are covered by CASREACT (see also Reaction Databases). CASREACT has been indexed since 1985 and currently holds 2.9 million chemical reactions from the chemical and patent literature,... 

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). 

The concept of superatoms included in the SMD format permits a structured representation of (large) molecules and reactions. Furthermore we believe that this concept indicates a possible way of handling generic structures and Markush formulas. We do not have a final solution for these problems yet, but promising attempts are under investigation. 

Scheme 6.2 Generic representation of poly(arylene ether) backbone structure.

The human oxytocin receptor gene was isolated and characterised in 1994 [122], heralding the development of modern cloned receptor screening. The oxytocin receptor belongs to the Family A series of G-protein coupled 7-transmembrane receptors (GPCRs). A schematic representation of the generic structure of 7TM receptors is shown in Figure 7.3. 

Although the linearity of the chain-rule differential expressions (10.5) confers primitive affine-type spatial structure on thermodynamic variables, it does not yet provide a sense of distance or metric on the space (other than what might be displayed in an arbitrarily chosen axis system). In order to bring intrinsic geometrical structure to the thermodynamic space, we need to define the scalar product (R RJ) [(9.29)] that dictates the spatial metric on Ms- The metric on Ms should reflect intrinsic physical properties of the thermodynamic responses, not merely generic chain rule-type mathematical properties of their differential representation. At the same time, we must exhibit how the space Ms is explicitly connected to the physical measurements of thermodynamic responses. Because such measurements assign scalar values to physical properties, it is natural to associate each scalar product of Ms with the scalar value of an experimental measurement. How can this be done ... 

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