The Y11 and Y18 compounds were docked to the EBOV GP protein by AutoDock 4.2. The structural template of EBOV GP (Protein Data Bank: 5JQ3) was obtained from the RCSB Protein Data Bank (www.rcsb.org/pdb/home/home.do). Grid points covering EBOV HR2 were generated with AutoDock Tools to perform blind docking experiments. The box size was 80 × 80 × 80 points with a standard spacing of 0.375 Å. Docking simulations for the compounds were performed using the Lamarckian genetic algorithm (GA) and a protocol with 50 GA runs, an initial population of 300 randomly placed individuals, a maximum number of 25 million energy evaluations, a mutation rate of 0.02, and a crossover rate of 0.80. The resulting conformations, which differed by less than 2.0 Å in the positional root mean square deviation, were clustered together. The default values were used for all other parameters. All relevant torsion angles were treated as rotatable during the docking process to allow searching of the conformational space. After AutoGrid and AutoDock were run, the possible positions of the compounds on EBOV GP were obtained. The same procedure was conducted for the docking simulations of Y19 and Y20 with HIV-1 gp160 (PDB: 4TVP) and of Y3 and Y21 with influenza virus HA (PDB: 3LZG).

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