Words similar to autodock

Example sentences for: autodock

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Since most current docking programs treat the receptor and/or ligand as rigid objects, this represents an important cause of failure to predict the correct binding enzyme-substrate energies [ 18 ] . We address this problem by performing Molecular Dynamic (MD) simulations on HIV-1 protease-inhibitor complexed and using the resulting structures to calculate the binding energies by AutoDock, a ligand flexible docking program.
Docking calculations were carried out using AutoDock, version 3.0.
To calculate the binding energy with AutoDock, we first prepared the protein complexes by separating each snapshot recorded from MD simulations into one file containing the protease and the water molecules, and one file containing only the ligand.
Table 1shows that the correlation coefficient of the experimentally determined and calculated binding energies from AutoDock for the twenty-five protease-inhibitor complexes after protein-rigid docking was 0.38.
At the end of a docking job with multiple runs, AutoDock performed cluster analysis.