Before the tunnel analysis, three residue segments were removed from the MD snapshots (residues 365 to 372, 1333 to 1340, and 2301 to 2308). These segments were loose during the simulation and bind to the mouth of the s-glycoprotein tunnel. The tunnel extending through the s-glycoprotein trimer was characterized using HOLE v2.2.005. The vector for the HOLE calculation was defined by the centre points between the C-alpha atoms of the following residues: LYS 1034 and PRO 986 in all three subunits of the s-glycoprotein structure, and LYS 858, 1826, 2794 and PRO 810, 1778, 2746 in the MD snapshots. A sample rate of 0.9 Å was used, and the end radius was set to 10 Å. We analysed the tunnel radii and cut the segment going through the S1 domain until the first extreme tunnel bottleneck was reached; the distance at which this bottleneck was encountered varied between 60 and 80 Å depending on the structure or snapshot under consideration. The output of the HOLE was converted into the CAVER 3 PDB file format to enable discretization for CaverDock calculations. However, the tunnel predicted by HOLE for the s-gp structure contained disconnections that made it undiscretisable. Therefore, we remodelled this tunnel using CAVER 3.02, starting from C-alpha of Thr A 1009. The probe radius, shell radius, and shell depth were set to 0.7, 20, and 20, respectively. Finally, the selected tunnel parts were discretized into a series of discs using the discretiser tool with default settings.