When all input structures are ready for docking, start Virtual Screening by using AutoDock Wizard widget shown below.

On the first page select whether to run AutoDock locally or remotely (buzzword: cloud computing) using Opal Web Services Toolkit developed at National Biomedical Computation Resource (http://nbcr.net). The advantage of using Web Services over PBS Batch Job is that Web Services can be run from Windows or Mac OS X based PC, whereas PBS Batch Job require Unix/Linux cluster. On “Select Ligands” and “Select Macromolecule” page user selects ligands and macromolecule, correspondingly, from the list of available molecules in Navigator pane.

On “Run AutoGrid” page adjust grid box by dragging handles of the VTK box widget before running AutoGrid.

On “Run AutoDock” page user can select among four docking algorithms available in AutoDock 4.0 as well as modify docking parameters used in each algorithm.

“Analyze Results” page is presented at the end of Virtual Screening where binding energies are displayed. Users can sort/filter results or save them as CSV (comma-separated values) for further analysis with third-party spreadsheet programs.. We also provide option for plotting clustering histograms using matplotlib – python 2D plotting library. “Analyze Results” page can also be used to open DLGs (docking log files) from previous AutoDock runs.