Table 1.
Average running time, running time fold improvement, and memory usage of optimized ZDOCK versions.
Figure 1.
Success rate and hit count of original and optimized versions of ZDOCK for all test cases (A, B) and rigid-body test cases (C, D) of docking Benchmark 4.0.
ZDOCK 3.0.2f and 2.3.2f represent the optimized versions with receptor rotation and receptor/ligand switching turned off, while ZDOCK 3.0.2 and 2.3.2 represent the fully optimized versions of ZDOCK 3.0 and ZDOCK 2.3, respectively. Success rate is defined as the percentage of cases with hits (RMSD less than or equal to 2.5 Å when comparing with Cα atoms in the bound interface to corresponding Cα atoms in the prediction) for a given number of top-ranked ZDOCK predictions per test case, while hit count is the average number of hits across the set of cases for a given number of top-ranked ZDOCK predictions per test case.
Figure 2.
ZDOCK running time and grid size comparison for all 176 Benchmark 4.0 test cases.
(A) ZDOCK 3.0 running time versus ZDOCK 3.0.2 running time on a single 2.8 GHz processor; outlier test cases 2VIS, 1I4D, and 1N2C are labeled. (B) ZDOCK 3.0 grid size versus ZDOCK 3.0 running time for all test cases. Grid size is the product of the number of points in each dimension of the cubic grid, calculated based on the sum of the cubic grids calculated for the ligand and receptor individually. (C) ZDOCK 3.0.2 grid size versus ZDOCK 3.0.2 running time for all test cases. Grid size is the product of the number of grid points in each dimension, N_x*N_y*N_z, where N_x is calculated using the number of grid points for the receptor in the x dimension plus the number of points of the ligand grid in the x dimension (which is equal to the number of points for the y and z dimensions as the ligand is in a cubic grid), and likewise for the other dimensions N_y and N_z.
Figure 3.
Grid sizes and initial rotation of the receptor of test case 1I4D, front (lengthwise) view (left) and side view (right).
The outer (gray) box represents the grid for the receptor given by ZDOCK 3.0 and the gray molecule represents its corresponding centered orientation, while the blue molecule and black box represent the rotated and centered molecule and grid for ZDOCK 3.0.2. Grid dimensions for ZDOCK 3.0 are 140×140×140 = 2,744,000 cells, while the dimensions for ZDOCK 3.0.2 are 40×66×134 = 353,760 cells.