Table 1.
Successful binding mode reproduction of the 56 RNA-ligand complexes using different docking/scoring combinations with arbitrary cutoffs. The values in the brackets indicated the total number of complexes in that category. The values before the parentheses results satisfying C(5, 3.0Å), and the values in the parentheses were derived with the stringent criterion C(3, 1.5Å) (described in the Materials and Methods). The Glide XP mode could not obtain enough data with the stringent restraints, thus the VUS values and R2 were not available.
| GOLD 5.0.1 | AutoDock 4.1 | Surflex 2.415 | Glide 5.6 | rDock 2006.2 | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
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| GOLD Fitness | ChemScore | ASP | Autodock4.1 Score | Surflex-dock Score | GlideScore (SP) | Emodel (SP) | GlideScore (XP) | Emodel (XP) | rDock | rDock_solv | |
| Aminoglycoside [26] | 18 (9) | 13 (3) | 15 (9) | 1 (1) | 4 (2) | 12 (3) | 13 (3) | 4 (2) | 4 (2) | 13 (6) | 16 (8) |
| Small Molecule [30] | 23 (15) | 17 (10) | 22 (15) | 16 (9) | 21 (13) | 18 (13) | 18 (13) | 16 (11) | 15 (11) | 21 (13) | 25 (15) |
| X-ray crystal [36] | 29 (19) | 26 (13) | 29 (21) | 13 (8) | 17 (11) | 20 (9) | 21 (9) | 12 (8) | 12 (8) | 24 (16) | 29 (17) |
| NMR [20] | 12 (5) | 4 (0) | 8 (3) | 4 (2) | 8 (4) | 10 (7) | 10 (7) | 8 (5) | 7 (5) | 10 (3) | 12 (6) |
| Total [56] | 41 (24) | 30 (13) | 37 (24) | 17 (10) | 25 (15) | 30 (16) | 31 (16) | 20 (13) | 19 (13) | 34 (19) | 41 (23) |
| Overall Success Rate % | 73.21 (42.86) | 53.57 (23.21) | 66.07 (42.86) | 30.36 (17.86) | 44.64 (26.79) | 53.57 (28.57) | 55.36 (28.57) | 35.71 (23.21) | 33.93 (23.21) | 60.71 (33.93) | 73.21 (41.07) |
| VUS % | 78.11 | 65.48 | 70.17 | 43.30 | 55.22 | 65.41 | 66.01 | NA | NA | 63.09 | 73.13 |
| Score-binding affinity correlation R2 a | 0.25 | 0.03 | 0.29 | 0.22 | 0.05 | 0.10 | 0.14 | NA | NA | 0.15 | 0.18 |
a
excluding 1TOB, 2TOB and 1LVJ when calculating Pearson correlation coefficient