For peptide and antibody structures, CoDockPP is used as a docking engine. CoDockPP program provides a multistage FFT-based strategy for both global docking and site-specific docking. An angle interval of 15º is used for rotational sampling, and a spacing of 1.2 Å is adopted for fast Fourier transform (FFT) translational search. The top binding modes are clustered with ligand root mean square deviations (L_RMSD) cutoff of 3.0 Å in global docking and 2.0 Å in site-specific docking.

Figure D shows an example of antibody docking. The spike protein docked with antibody. The spike protein is colored in gray and the predicted structure of Top 1 is colored in pink.