Indirect encoding

Input/Output sequence encoding methods (see Table 9.1) PRF direct encoding of residue profile a = a-helix fi = P-sheet C = random coil t = (5-reverse turn L = loop %AA = amino acid composition FEAT = indirect encoding of sequence features MF = memory factor dist = distance Map = Kohonen map (with dimensions). 

The various properties of molecules that can be used in a QSAR are often designed to quantitate the tendency of the molecules to participate in one of the fundamental types of intermolecular interactions electrostatic, hydrogen bonding, dispersion forces, and hydrophobic interactions. In addition, the possibility of steric interference with an interaction is considered. Other methods capitalize on the fact that the 2D structure of a molecule indirectly encodes its properties, instead generate descriptors without an explicit relationship to some physical property. 

A challenging task in material science as well as in pharmaceutical research is to custom tailor a compound s properties. George S. Hammond stated that the most fundamental and lasting objective of synthesis is not production of new compounds, but production of properties (Norris Award Lecture, 1968). The molecular structure of an organic or inorganic compound determines its properties. Nevertheless, methods for the direct prediction of a compound s properties based on its molecular structure are usually not available (Figure 8-1). Therefore, the establishment of Quantitative Structure-Property Relationships (QSPRs) and Quantitative Structure-Activity Relationships (QSARs) uses an indirect approach in order to tackle this problem. In the first step, numerical descriptors encoding information about the molecular structure are calculated for a set of compounds. Secondly, statistical and artificial neural network models are used to predict the property or activity of interest based on these descriptors or a suitable subset. 

Polar intermolecular interactions encoded in partition coefficients an indirect estimation of hydrogen-bond parameters of polyfunctional solutes. J. Phys. Chem. 1992, 96,1455-1459. 

Within the effects clause, there is no strong difference between participants and parameters both can be affected by the action. The distinction is intended to document a partial design decision. The participants exist or will be built as separate entities, with some direct or indirect interaction between them to realize the action. Together, the parameters represent information that is passed between the participants, encoded in a form not documented here, and possibly communicated differently. 

E. coli strains. E. coli 0157 H7 strains lack efal, but do encode toxB, a tnmcated version of the efal gene. A toxB mutant exhibits reduced adherence to cultured epithelial cells (Stevens et ah, 2004). However, toxB had an indirect effect on adherence to epithelial cells by modulating the production and secretion of proteins that play a role for A/E formation in EHEC. The receptors for Efal and ToxB have not been identified and their true role in vivo is unknown. 

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