Autodock VINA

Among these, Autodock, Autodock Vina, Dock, and FRED are freely available for academic users. 

Trott O, Olson AJ (2010) AutoDock Vina improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31 455-461. doi 10.1002/jcc.21334... 

These files are converted into. pdbqt format (as they are needed by Autodock Vina) through MGL tools. Click on the autodock icon on your desktop to open the workspace. Go to File menu on the top and then to Read molecule and from there browse the protein. pdb file into the workspace (Fig. 4.38). 

After preparing the pdbqt files for target and ligand, we can use either Autodock or Autodock Vina. 

How is Autodock program different from Autodock Vina ... 

Trott O, Olson AJ (2010) AutoDock Vina improving the speed and accuracy of docking with a... 

Before input files can be used for virtual screening, they must be converted to the PDBQT file format suitable for docking with AutoDock Vina [11]. 

Click on the Maximize button under Vina Search Space and then click on the Forward button. This starts AutoDock Vina and docks each ligand, one by one, to neuraminidase (2BAT). It takes less than 20 min to complete this virtual screening on a PC mentioned in Subheading 2.1 (fcc Note 4) (Fig. I). 

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