Protein Structure from Scientific Research

Representative systems show diversity in ligand structures, and such predicted diversity is related to the properties of the binding pocket. For a deep and narrow binding pocket such as for the TYK2 protein (shown in the surface representation, top panel), DiG predicts highly similar binding poses for the ligand (in atom bond representations, top panel). For the P38 protein, the binding pocket is relatively flat and shallow and predicted ligand poses are more diverse and have large conformational flexibility (bottom panel, following the same representations as in the TYK2 case). The average r.m.s.d. values and the associated standard deviations are indicated next to the complex structures.

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