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Fig. 7 | Journal of Cheminformatics

Fig. 7

From: Binding mode information improves fragment docking

Fig. 7

Examples of rescoring failures and successes. On the left: the docked fragment (green) and the reference molecule (magenta). On the right: comparison of the native pose (transparent cyan sticks), the pose selected by rescoring (green) and that of the corresponding reference (magenta). a Docking of 2-Amino-1,2,3,4-tetrahydronaphthalen-1-ol (HET ID: TTL, PDB ID: 2AN5) in the phenylethanolamine N-methyltransferase (P11086; PDB ID: 3KQT). GRIM rescoring uses a fragment reference (HET ID: CTL; PDB ID: 2AN3). b Docking of 3-phenyl-5-(1H-pyrazol-3-yl)isoxazole (HET ID: D25; PDB ID: 2VCQ) in the hematopoietic prostaglandin D synthase (O60760; PDB ID: 2VCZ). ROCS rescoring uses a fragment reference (HET ID: VC3; PDB ID: 2VCZ). c Docking of N-(phenylcarbonyl)-beta-alanine (HET ID: BYA; PDB ID: 3FGD) in the thermolysin (P00800; PDB ID: 4H57). GRIM rescoring uses a drug-like ligand reference (HET ID: UBT; PDB ID: 3T8G)

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