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, 31 (2), 455-61

AutoDock Vina: Improving the Speed and Accuracy of Docking With a New Scoring Function, Efficient Optimization, and Multithreading

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AutoDock Vina: Improving the Speed and Accuracy of Docking With a New Scoring Function, Efficient Optimization, and Multithreading

Oleg Trott et al. J Comput Chem.

Abstract

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user.

Figures

Figure 1
Figure 1
Weighted scoring function term combinations. Steric interactions; steric and hydrophobic interactions; and steric and hydrogen bonding interactions, using weights from table 1
Figure 2
Figure 2
RMSD of the predicted bound ligand conformation from the experimental one, showing the values for Vina and Autodock. The color encodes the number of active rotatable bonds
Figure 3
Figure 3
RMSD of the predicted bound ligand conformation from the experimental one. (Red +) Autodock; (Green ×) Vina. Abscissa shows the number of active rotatable bonds
Figure 4
Figure 4
Time, in minutes, taken by the multi-threaded Vina run, as a function of the number of heavy atoms in the ligand. The color encodes the number of active rotatable bonds
Figure 5
Figure 5
The fraction of the 190 test complexes for which RMSD < 2Å was achieved by AutoDock and Vina
Figure 6
Figure 6
Average time, in minutes per complex, taken by AutoDock, single-threaded Vina and Vina with 8-way multithreading. Machines with two quad-core 2.66GHz Xeon processors were used in the experiment. The time for AutoDock does not include the necessary initial AutoGrid run
Figure 7
Figure 7
Experimental and predicted free energies of binding (kcal/mol) for (a) AutoDock, (b) Vina. The color encodes the number of active rotatable bonds

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