Murcko scaffold

Fig. 2.27 A comparison of Bemis Murcko scaffold and ChemScreener scaffold...

The scaffold extractor generates scaffolds, extended scaffolds and frameworks. The extended scaffolds, imlike the conventional Bemis Murcko scaffold [72], retain cormection information and are used in focussed library synthesis (Fig. 2.27). 

Figure 21.10 The network map in (a) shows the connections between the Murcko scaffolds. All fragments contain compounds with a significantly shifted activity distribution in the HTS screen versus the entire compound collection (green nodes). The D ax shift and the probability (p-value of the shift) of the fragment is plotted in (b). The color gives the number of compounds associated...

Bemis and Murcko (10) analyzed known drugs in an effort to identify common features and scaffolds, which could be used to bias fragment libraries toward drug-like structures. An optimal molecular complexity was also discussed by Hann and coworkers... 

Fig. 15.4-6 Analysis of privileged scaffold-target matrix of monoamine CPCR ligands. For each CPCR ligand assigned in the MDL Drug Data Report (MDDR) database to a specific monoamine CPCR subtype, the Bemis-Murcko frameworks were generated. The lists of frameworks were then combined and duplicates were eliminated. The comprehensive list of unique frameworks define the row vector of the matrix, and the CPCR subtypes were arranged to the column vector. The matrix...

Figure 2 Murcko structures for bioactive molecules, (a) Quinoline as Murcko framework of bioactive aminoquinolines after removing side chains and (b) different levels of structural simplification of Hsp90 inhibitor NVP-AUY922 provide different structural levels of scaffolds.

Scaffold abstraction approaches like topological frameworks or reduced graphs were first proposed by Bemis and Murcko [28] and further explored by Xu and Johnson [29]. Groupings into series by some fuzzier similarity are obtained by using different abstraction levels for atom types, bond types, and ring topologies. 

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