Full combinatorial method

The full combinatorial algorithm confirms the validity of the ad hoc parameters, AH, AH", and 1) introduced with the use of the greedy algorithm to model Tt, and and p, respectively. The rationale for these three ad hoc parameters wUl be explained in the next section. The descriptimis obtained with the full combinatorial method, either pure MCI or semiempirical, are collected in Tables 7.9 and 7.10. 

The zero-level descriptors obtained with the full combinatorial method are collected in Tables 7.11 and 7.12, while the best full combinatorial semi-random descriptors are collected in Tables 7.13 and 7.14. 

The dielectric constant is the only experimental parameter that can here be used, as it is the only property that has N = 63. Comparison between Tables 7.8 and 7.10 shows the noticeable improvement achieved by the full combinatorial method over the greedy method, especially at the Y level. The correlation vector of descriptor (Table 7.9) used to model this property and to obtain Fig. 7.2 is ... 

The full combinatorial exploitation of 3.25 requires an assessed SP synthetic method to build and decorate the scaffold for SP library generation ... 

In contrast with the split/pool method, parallel synthesis does not require encoding, produces discrete compounds in measurable quantities, and allows for collection of a full SAR. It is becoming increasingly popular among other combinatorial methods. 

The best Kp pp-odd) fs greedy descriptor can be seen in Tables 7.7 and 7.8 and the best full combinatorial Kp(pp-odd) /fg ° descriptor is shown in Tables 7.9 and 7.10 (here only ij/E and Z are S - or configiuation-dependent). The fuU combinatorial method, achieves to find also a good five-index semi-empirical descriptor,... 

Once mutant proteins are produced, either rationally or combinatoriaUy, the new proteins need to be characterized in order to determine the full effects of the underlying mutations. It has been repeatedly shown that improvements in one trait can come at the cost of another trait. This can be especially true in combinatorial methods, where you get what you screen for. Once the effects of the mutations are understood, the process is repeated in order to produce further improvements in the protein of interest. In some cases, it may also be useful to combine the methods or protein engineering. For example, combinatorial methods may suggest an area in the protein that should be further investigated using site-directed mutagenesis. 

Today an increasing importance of qualitative analysis can be stated in certain fields. This is due to an increasing number of materials under study, especially active agents of interest on the one hand, and the many and diverse ways of synthesis (e.g., by combinatorial chemistry) on the other hand as well as the increasing demands on quality. Because analytical laboratories in research and routine control would be overtaxed in their capacity if full quantitative analyses were done generally, screening methods become more and more significant. 

All these techniques create genetic diversity by recombination and point mutations and are well developed. However, insertions and deletions (indels) are also important types of mutation which are probably underrepresented in many conventional mutagenesis strategies. Methods for incorporation of indels in predefined positions in a combinatorial manner have been developed.Although there are some published studies on their use in the directed evolution of biocatalysts,the full potential of these newer methods of gene mutation for enzyme improvement are yet to be demonstrated. 

The split-and-pool synthesis not only simplifies the complexity of the combinatorial synthetic process, but also offers additional important benefits. To undertake a full range of solid-phase chemical reactions, elaborate reaction conditions are needed for some chemical transformations. These include, but are not limited to, low temperature and inert atmosphere conditions. Parallel synthesis of a thousand compounds requires handling of a thousand reaction vessels. The timely addition of sensitive reagents (e.g., butyl lithium) at low temperature (—78°) under inert atmosphere during parallel synthesis is not a trivial task. It can be done if sophisticated automated synthesizer equipment is designed to handle and tolerate such reaction conditions. Such a synthesis can alternatively be performed easily in a manual fashion using a split-and-pool method that requires only a limited number of reaction vessels. Examples from Nicolaou s17 and Schrei-ber s18,19 laboratories have shown that the split-and-pool method is the methodology of choice for the synthesis of complex and diversity-oriented combinatorial libraries. 

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