Fig. 3: The 3D poses and interaction patterns of ligand molecules with the target proteins (PDB IDs: 3CQW and 1L2S). | npj Drug Discovery

Fig. 3: The 3D poses and interaction patterns of ligand molecules with the target proteins (PDB IDs: 3CQW and 1L2S).

From: Interaction-constrained 3D molecular generation using a diffusion model enables structure-based pharmacophore modeling for drug design

Fig. 3: The 3D poses and interaction patterns of ligand molecules with the target proteins (PDB IDs: 3CQW and 1L2S).

a, g Reference ligands for 3CQW and 1L2S, respectively. b–f and h–l The molecules generated for 3CQW and aL2S, respectively. The five generated molecules for each target protein are displayed in descending QED order; those that satisfy all the interaction conditions used during the generation process and for which synthetic routes are identified through retrosynthetic analysis are selected through screening. Each molecule is shown with its QED score and its Tanimoto similarity69 relative to the reference molecule, wich are calculated using the RDKit fingerprint70. Figures generated using PyMol.

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