Fragment screening

The smaller, less complex nature of fragments increases the probability of finding a match to a receptor moreover, instances have shown that removing complexity by screening fragments can succeed where HTS has failed [6]. 

Screening fragments requires more sensitive detection methods, but at the same time these methods provide invaluable information in the development from hits to drug candidates. 

A pitfall of screening fragments by all biophysical methods, such as those already described, is that they do not reveal whether a fragment that is found to bind to a target protein has an effect on the normal function of the protein (see below). This is why biochemical data should be collected in parallel with biophysical data whenever possible. 

If a database structure contains a fragment isomorphic to one of the screen structures, the corresponding bit is set to 1. Consequently, every bit set in the query molecule must appear in the database molecule bit vector to ensure the presence of the corresponding screen fragment. Comparing the screen vectors of query and database molecules can reduce the search effort dramatically if the screen fragments have been selected adequately. 

Keywords Biophysical screening Fragment-based drug discovery Inhibitor Protein-protein interactions Structural biology... 

Fig. 15.1-6 Selected fragment screening experiment applied to proteases and kinases. In their landmark study, Fesik et al. equilibrated hydrophobic molecules with stromelysin and detected binding by shift of NMR signals, retrieving structural information from the initial study [66]. Other studies screened fragment collections using...

Fig. 11. The use of Southern blotting and radioactive probes for screening fragmented DNA...

The screen generation process identifies specific structural features present in the structures. These features are called screens or screen fragments and are described in more detail below. The screens generated for query structures are formulated into a screen search logic expression and sent to the screen search phase. Screens generated for file structures are sent to the appropriate file loading systems. 

Figure 28 Illustration of augmented atom screen fragments...

CS 1 3 - 3 2 2 3-2 Figure 29 Illustration of linear sequence screen fragments... 

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