Three-dimensional Geometry-based Models

Often, all alignment-based methods and molecular field and potential calculations are classified as pharmacophore perception techniques. We will include most of these methods in this review however, when using the term pharmacophore model, we will be referring mainly to one specific type of perception, namely three-dimensional feature-based pharmacophore models represented by geometry or location constraints, qualitative or quantitative. An extrapolation of the pharmacophore approach to a set of multi-dimensional descriptors (pharmacophore fingerprints) has been developed mostly for library design and focusing purposes [3-8]. 

A distance geometry approach using a three-dimensional structure-directed QSAR method (REMOTEDISC)was employed to analyze the inhibition of [ H]diazepam binding by 29 benzodiazepines (115). The results of the method, which uses three-dimensional structure, conformational energies, and atom-based physiochemical properties to model the receptor binding cavity were based on Equation 5.12. 

The model for the geometry description in MOREX contains a complete three dimensional, parametrized description of conveying- and kneading elements. Based on this model a surface mesh can be exported to the BEM-software. For the structure of these meshes the cross section can be seen in Fig. 5.36. Additionally the visualization of the screws in MOREX is based on these meshes. The boundary conditions for the numerical methods as well as the velocity profile at the flow channel inflow and the viscosity can be given in a specified module in MOREX, resp. are overtaken from a previous MOREX calculation. 

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