AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
Fig 12
Docking volume definitions for docking programs (left) and input conformer sources used for docking (right).
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).