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Fig. 1 | Journal of Cheminformatics

Fig. 1

From: Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores

Fig. 1

Screening protocol developed to select selective pharmacophores for agonist ligands and selective pharmacophores for antagonist ligands using LigandScout. The example presented here started with a pharmacophore generated with agonist ligands containing 2 aromatic rings (blue square) and 3 hydrophobic groups (yellow square). The pharmacophore was retained if only agonist ligands were retrieved in the screening 1 (with the Max. number of omitted features set to 0, which means that only ligands mapping the 5 pharmacophore features are considered as hits). Then, we tried to identify non-essential feature in the screening 2 by setting the Max. number of omitted features to 1 (which means that the ligands mapping 4 of the 5 pharmacophore features are considered as hits). A second agonist pharmacophore was defined by disabling the pharmacophore feature identified as non-essential. The agonist pharmacophore 2 was validated if the hits of the screening 3 (with the Max. number of omitted features set to 0) were only agonist ligands. This protocol was applied to each pharmacophore until 3 pharmacophore features were retained or until no non-essential feature could be identified

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