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. 2021 Feb 1;17(2):e1008309. doi: 10.1371/journal.pcbi.1008309

Fig 12. Docking volume definitions for docking programs (left) and input conformer sources used for docking (right).

Fig 12

For AutoDock Vina and iDock a box of sizes 20 Å ✕ 20 Å ✕ 20 Å was set, with a center in the center of mass of the ligand (pane A), while for the rDock it is defined as a volume around the known ligand at the maximum distance 10 Å from the ligand atoms (pane B). Three sources of ligand conformers were tested in docking: native pose extracted from the experimentally determined structure (pane C) and conformations generated de novo by two programs: OpenBabel and Balloon (pane D).