Multi-level analysis of intrinsically disordered protein docking methods.

• Structure prediction for intrinsically disordered protein complexes benchmarked. • Proposed and used multiple levels of model evaluation metrics. • IDP-LZerD, CABS-Dock, and Alphafold-Multimer were benchmarked. • Binding residues are in general well identified by the three methods. • Alphafold-Multimer performed well at atom level but still room for improvement. Intrinsically Disordered Proteins (IDPs) are a class of proteins in which at least some region of the protein does not possess any stable structure in solution in the physiological condition but may adopt an ordered structure upon binding to a globular receptor. These IDP-receptor complexes are thus subject to protein complex modeling in which computational techniques are applied to accurately reproduce the IDP ligand-receptor interactions. This often exists in the form of protein docking, in which the 3D structures of both the subunits are known, but the position of the ligand relative to the receptor is not. Here, we evaluate the performance of three IDP-receptor modeling tools with metrics that characterize the IDP-receptor interface at various resolutions. We show that all three methods are able to properly identify the general binding site, as identified by lower resolution metrics, but begin to struggle with higher resolution metrics that capture biophysical interactions. [ABSTRACT FROM AUTHOR]