Sentence examples for of each docking from inspiring English sources
One challenge in parallelizing AutoDock for a cluster environment is that the program can generate significant network I/O during the loading of grid maps at the beginning of each docking, and when writing log files as dockings finish.
As AutoDock reports the best docking solution for each GA run and also performs a cluster analysis in which the total number of clusters and the rank of each docking mode (cluster rank) is reported, in 7 out of 10 docked conformations obtained by the clustering analysis at 2.0 Å, the carbonyl group of the lactone ring is found closest to the hydroxyl group of Thr1.
A total of 50 structures were generated at the end of each docking run.
The resulting models of each docking run were clustered with a 5 Å cut-off and the clusters ranked based on the average HADDOCK score calculated over the best four members of each cluster.
Using our default configuration, the running time of each docking step (20 rounds) is about three hours in a quad core computer (using the four cores at full capacity) and the whole process to get a pMHC complex (D1-EM-D2) takes about 7 hours in the same scenario.
At the end of each docking simulation an output file is generated.
The control towers and ancillary buildings of each dock force you to stay alert until the moment you bring your ship in to touch down gently on the centre of the landing pad, when clamps grab the ship and your engines are powered down.
The hDHFR ligands in cluster c had hydrogen bonds (E30-OE1, E30-OE2, V115-0, in-0 in green dotted lines) and van der Waals forces shown by a blue arc (I60-CAR, F31-RING) revealing that binding interactions of each docked pose within cluster c were similar.
Figure 6 illustrates the RMSD (root-mean-square deviation) values of the best conformations in respect to the lowest distance from the native conformation of the ligand for each dock.
Each docking run consisted of 100 independent docks with 1000 iteration cycles.
Because each docking simulation is made of 10 runs, we obtain 31,000 docking results for each ligand.
