Table 1. Docking Success Ratesa.
| RNA typeb | I (9) | II (1) | III (2) | IV (2) | V (2) | VI (1) |
|---|---|---|---|---|---|---|
| redockingc | 9 | 1 | 2 | 2 | 2 | 1 |
| apo-dockingd | 2 | 1 | 0 | 0 | 1 | 0 |
| deformed gridse | 7 | 1 | 0 | 0 | 1 | 0 |
a
The number of complexes is given for which a ligand configuration with ≤2.5 Å rmsd from the native structure was found on the first rank of the largest cluster of docking solutions.
b
The number of complexes for each RNA type is given in parentheses. I, 16S E. coli rRNA; II, Aptamer RNA; III, 23S H. marismortui rRNA; IV, 16S T. thermophilus rRNA; V, HIV-1 TAR RNA; and VI, Thi-box riboswitch RNA.
c
Docking the ligand back into its holo RNA structure.
d
Docking the ligand into an apo RNA structure.
e
Docking the ligand into a deformed grid whose potential values were calculated based on an apo RNA structure and which was subsequently deformed following RNA movements from the apo to the ligand's holo RNA structure.