Feature definitions

At the beginning of this chapter we will look into the different automated alignment methods as correct alignment is the first and most important prerequisite for a successful pharmacophore identification process. Further, we will elaborate how essential issues of pharmacophore modeling such as conformational search, pharmacophore feature definitions, compounds structure storage and screening are handled by various available software packages. 

Catalyst models (hypotheses) consist of sets of abstract chemical features arranged at certain positions in the three-dimensional space. The feature definitions are designed to cover different types of interactions between ligand and target, e.g. hydrophobic, H-bond donor, H-bond acceptor, positive ionizable, negative ionizable. Except in some special cases, different chemical groups that lead to the same type of interaction, and thus to the same type of biological effect,... 

The Accelrys implementation of pharmacophore fingerprint descriptors is called 3D Keys. This application is based on standard Catalyst feature definitions and is a part of the Cerius2 software package [7]. 

The chemical feature definitions described in the following sections are all categorized into hydrogen bond interactions, which are described as layer 3 features, and also into charge interactions and lipophilic interactions, which are represented as level 4 features. All current layer 4 features are represented as points with a tolerance radius forming a sphere, whereas layer 3 features are represented by vectors. The chemical feature definitions are specified in Daylight SMARTS notation [37] (listed in detail in Table 6.2) and directly imported into... 

Gravure Able to print on wide variety of substrates. High speed. High quality/feature definition. High set-up costs. Being developed for roll-to-roll printing applications. 

Fig.9 Scanning microphotxjgraph of photoresist patterns. (a) without D4-CEL layer, (b) with D4-CEL. Feature definition is enhanced in submicron structure.

Represented as tolerance spheres, no explicit charges necessary Feature definitions as SMARTS or boxed algorithms, adjustment of feature specific parameters and geometric constraints... 

Fig. 4.2 Catalyst feature definition applied to a simple molecule, illustrating the inclusion of receptor site-points in the pharmacophore definition.

Host and guest are two organic molecules or ions, which are capable of mutual association. Herein, we use the term host-guest complexation to refer to a class of molecular association and recognition phenomena which differ from both traditional organic reactions and solvation. In contrast to the common chemical reactions, these phenomena do not involve formation or cleavage of covalent bonds in contrast to the bulk solvent-solute interactions, they feature definite stoichiometry and at least a certain degree of specificity. 

The library, containing standard elements, can be tailored to the user s requirements for production and form elements. This ensures consistency between product development and the ability to manufacture the product. Therefore, only standard elements that match those of available production capabilities are made available. Feature definition, in the sense of concurrent engineering, is an activity in which all aspects of product creation in design, production, and further product life phases are considered. 

Figure 4-13 Three-level approach for form feature definition.

The types of form features discussed above include the important ones although the list cannot be complete. A variety of other feature definitions such as helical protrusions and cutouts, teeth, etc., can be available to modify shapes of parts. 

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