Fig. 3: Case study of generated molecules involving 3D binding mode and 2D similarity with active compounds.
From: Generation of 3D molecules in pockets via a language model
Six cases are selected based on the docking scores of generated molecules and their similarities to reference active compounds. a,b, Cases with high similarity and good docking scores. c,d, Cases with high similarity but poor docking scores. e,f, Cases with low similarity but good docking scores. The reference binding mode is based on the crystal structure from the PDB. The Lingo3DMol conformation represents the generated conformation, while the GlideSP redocking conformation was obtained by docking the generated compound into the pocket using Glide with specific parameters (that is, docking_method:confgen and precision:sp). The most similar known active compound to the generated molecule is also displayed, noting that it may not necessarily be the reference compound observed in the crystal structure. The information provided includes the PDB ID for the reference binding mode, the Tanimoto similarity between the Bemis–Murcko scaffolds of generated molecule and its most similar active compound, and the GlideSP redocking score.
