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Docking experiment

This subset was further investigated using the slower modeling methods to try to identify potential actives, known as plausible hits. An example of a molecule selected from the results of a docking experiment is shown in Fig. 4.8. This molecule had a similarity score of 0.93 to an active and is shown docked with the typical kinase inhibitor binding pattern. Both the active and the plausible hit are not drug-like from a medicinal chemistry perspective, but this example demonstrates well how the Feature Tree descriptor captures similarity between two molecules. [Pg.95]

Fig. 4.8 (a) A plausible hit molecule (top) selected after completion of docking experiments on the small subset of molecules. A similar known active is shown beneath, (b) The docking pose of the plausible hit in the active site of CDK2 as predicted with the... [Pg.96]

This chapter aims to present a very practical description of how to set up in silico docking experiments. Many problems and pitfalls that can be encountered during these experiments will be discussed. Because a thorough discussion of the theoretical background of the algorithms is beyond the scope of this chapter, references to important papers describing fundamental aspects are specifically mentioned in the text. [Pg.64]

Peluroside A was the first microtubule stabilizing agent whose conformation has been determined bound to microtubules (those of Paclitaxel and Epothilone were determined in non-microtubular tubulin [5, 12, 38, 91]). In the bound state, the NMR data, assisted by molecular mechanics calculations and docking experiments, indicated that only one (that present in water, B) of the two major conformations existing in water solution is bound to microtubules (a-tubulin). A model of the binding mode to tubulin has also been proposed [27], involving the a-tubulin monomer, in contrast with paclitaxel, which binds to the p-monomcr. [Pg.84]


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Cross-docking experiments

Docking

Docks

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