Substructure, definition

The Reasoner combines evidence from all sources and makes deductions from this evidence. The combination of evidence results in a single "confidence level" for each substructure. These confidence levels designate the degree to which the evidence supports the presence of the substructure in the unknown compound. They range from -100% (substructure definitely absent), through 0% (no information), to +100% (substructure definitely present). The confidence levels are ultimately derived from statistical analysis of representative spectral libraries. Details of the generation and propagation of confidence levels will be described in a separate report.(28)... 

Figure 10.3-54 illustrates how the reaction center is derived from the disconnection of the strategic bond and which additional bond spheres are considered in the definition of the reaction substructure search queiy. 

Contrary to widespread opinion, the value of Ea is not a constant quantity. As was proved previously [52], the value of E is variable, since it depends on the ordering of macromolecules in the amorphous material of the fiber. At the same time, one can suppose that this ordering will be affected by the specificity of the fine structure of the fiber, and particularly by the type of substructure of the fiber. The relationship determining the modulus Ea appropriate for a definite type of fiber substructure can be derived from Eq. (11) when appropriate values of A are assumed. In the case of the microfibrillar substructure, i.e., for A < I, typical of PET fibers stretched, but not subjected to annealing, this equation has the form [52] ... 

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. 

Webster s definition for database is a large collection of data in a computer, organized so that it can be expanded, updated, and retrieved rapidly for various uses. An LC/MS database established for drug impurities contains multi-dimensional information such as relative retention times, UV spectra, molecular mass and substructural information. In order for the information to be updated and expanded, the methods used for information collection need to be unified. A generic LC/MS method allows relevant information to be collected in a consistent... 

Each molecular transformation applied by Leatherface is specified by a SMARTS definition followed by a series of instructions that specify how the substructure matched by the SMARTS is to be modified. The first example shows how neutral carboxylic acids are converted to their more physiologically relevant anionic forms. The Pit instruction indicates that a single proton is to be removed (—1) from the atom matching the third atom in the SMARTS. 

Leatherface allows definition of atom types that can be used to specify more complex SMARTS patterns. This is done in a separate input file and can lead to a more readable specification of substructure. Neutral aliphatic amines can be defined as follows ... 

One might fear that the traditional descriptors are whole molecule properties that cannot distinguish the details of important substructural differences. It is difficult to quantify the wholism of a descriptor. A qualitative definition might be that a whole molecule property is one in which small bioisosteric... 

CATS3D was not only successful in scaffold hopping on the basis of the definition above (Meqi). We also observed a substructure hopping , which might be seen as an equivalent to more traditional bioisosteric replacement strategies. It seems that the CATS descriptor family represents molecules in a way that allows a combination of scaffold hopping and substructure hopping at once. This can result in a selection of molecules which would not be considered similar by other methods such as the MACCS keys. 

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