Table 3.
Performance of the two-stage docking protocol when using AIRs based on experimental information: the r.m.s.d values from the reference and fraction of native contacts for the top ten docking solutions of the top ranking cluster both selected based on the HADDOCK score
| r.m.s.d (Å) |
Fnate | CAPRIf *,**,*** | ||||
|---|---|---|---|---|---|---|
| Totala | Interfaceb | DNAc | Proteind | |||
| ‘Easy’ | ||||||
| 1by4 | ||||||
| Bound rigid | 0.410.08 | 0.340.07 | 0.000.00 | 0.380.07 | 0.890.02 | 0,0,10 |
| Unbound rigid | 4.330.72 | 4.010.53 | 1.410.00 | 4.660.73 | 0.110.04 | 4,0,0 |
| Unbound flex | 6.722.10 | 5.871.71 | 1.900.19 | 6.982.21 | 0.170.05 | 5,0,0 |
| DNA lib | 5.522.43 | 4.912.32 | 1.610.14 | 5.852.46 | 0.270.09 | 4,3,0 |
| 3cro | ||||||
| Bound rigid | 0.320.16 | 0.380.19 | 0.000.00 | 0.440.22 | 0.850.09 | 0,0,10 |
| Unbound rigid | 3.790.60 | 3.510.63 | 3.700.00 | 3.500.83 | 0.150.05 | 10,0,0 |
| Unbound flex | 3.570.63 | 3.290.68 | 2.860.30 | 3.190.68 | 0.270.07 | 6,2,0 |
| DNA lib | 2.890.40 | 2.620.73 | 2.080.21 | 2.960.43 | 0.400.06 | 3,7,0 |
| ‘Intermediate’ | ||||||
| 1azp | ||||||
| Bound rigid | 0.330.07 | 0.310.07 | 0.000.00 | 0.110.00 | 0.920.03 | 0,0,10 |
| Unbound rigid | 7.122.06 | 7.092.25 | 3.250.00 | 3.580.02 | 0.020.02 | 0,0,0 |
| Unbound flex | 6.902.00 | 6.682.26 | 2.870.32 | 3.640.13 | 0.040.04 | 0,0,0 |
| DNA lib | 4.560.79 | 4.000.45 | 1.830.26 | 3.760.16 | 0.100.04 | 5,0,0 |
| 1jj4 | ||||||
| Bound rigid | 0.390.10 | 0.400.09 | 0.000.00 | 0.100.03 | 0.820.07 | 0,0,10 |
| Unbound rigid | 4.230.37 | 4.760.48 | 3.190.00 | 1.470.05 | 0.090.02 | 3,0,0 |
| Unbound flex | 4.250.43 | 4.550.58 | 3.190.21 | 2.400.02 | 0.160.07 | 6,0,0 |
| DNA lib | 3.220.30 | 3.620.38 | 2.380.14 | 2.370.05 | 0.210.07 | 9,1,0 |
| ‘Difficult’ | ||||||
| 1a74 | ||||||
| Bound rigid | 0.060.01 | 0.070.01 | 0.000.00 | 0.010.00 | 0.840.01 | 0,0,10 |
| Unbound rigid | 5.430.99 | 6.880.97 | 7.440.00 | 1.680.14 | 0.040.02 | 0,0,0 |
| Unbound flex | 4.950.38 | 6.300.46 | 7.120.32 | 1.840.14 | 0.140.04 | 8,0,0 |
| DNA lib | 2.720.25 | 3.370.32 | 3.760.19 | 1.780.12 | 0.240.05 | 9,1,0 |
| 1zme | ||||||
| Bound rigid | 0.480.11 | 0.460.08 | 0.000.00 | 0.010.00 | 0.790.06 | 0,0,10 |
| Unbound rigid | 6.290.64 | 5.490.68 | 4.280.00 | 5.670.61 | 0.060.03 | 0,0,0 |
| Unbound flex | 6.150.62 | 5.290.59 | 4.680.33 | 5.880.27 | 0.120.06 | 4,0,0 |
| DNA lib | 5.270.62 | 4.630.80 | 3.350.13 | 5.550.48 | 0.150.04 | 8,0,0 |
Average all heavy atom r.m.s.d values from the reference structure (Å, standard deviation in subscript) calculated over:
aThe entire complex.
bThe interface.
cThe DNA only for the 10 top ranking solutions.
dThe protein only for the 10 top ranking solutions.
The r.m.s.d values are reported for; bound rigid-body docking (bound rigid); unbound rigid-body docking (unbound rigid), semi-flexible refinement (unbound flex.) starting from canonical B-DNA; unbound semi-flexible docking using a library of custom-built DNA structural models as input (DNA library).
eFnat is the fraction of native contacts.
fNumber of one-, two- and three-star CAPRI ranked solutions obtained in the top 10 solutions.