Fragment databases

Large, diverse and fragmented databases (which are not readily comparable) are generated by in vivo studies. 

GROUPBUILD Randomized build-up Fragment database Entropic and Generates Rotstein and... 

When the measured value for hexazinone was published (Yanase, 1992), the value for the dioxo-triazo fragment turned out to be -2.79 when allowance was made for its electronic interaction with the tertiary amino substituent. This is in good agreement with the prior estimate, and so the value appears in the latest fragment-database. The CLOGP calculation is, perforce, very good 1.85 vs. the measured 1.85. 

Fig. 4.13 (a) Workflow of a Feature Tree fragment space set-up. The underlying fragment database can be derived from retrosynthetic analysis (RECAP) of compound databases (WDI) and/or from a selection of reagents from vendor databases (ACD). In addition, chemical rules for allowed fragment combi-... 

Fragment-based programs employ molecular building-blocks from a fragment database that contains virtual synthons from commercially or synthetically available compounds or from virtual retrosynthetic decomposition of a compound database. The bonds cleaved during the retrosynthetic dissection process are not necessarily the ones that will be made during the actual synthesis. For example, the formation of a tertiary amine in the reaction shown in Figure 7.2 can be performed in different ways. Typically, retrosynthesis... 

Surf descriptors are computed for that fragment and stored within the fragment database. 

Depending on the animal models and toxicity endpoints of interest, the results might be in large, diverse, and fragmented databases that are not readily comparable. 

A set of over 2200 bioisosteric functional groups, linkers, and core scaffolds was extracted from Bioster 2001.1 and used in an unbiased validation of the fragment database of the IBIS drug discovery software [20]. 

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