Figure 6

DINC webserver. A webserver implementation of DINC is available at http://dinc.kavrakilab.org. The webserver takes as input a protein structure in pdb format and a ligand structure in mol2 format. Center and dimensions of the AutoDock grid, that encompasses the binding site, are specified. Both can either be specified in absolute terms or by using other options. For example, the grid dimensions can be specified based on the ligand as described in the Webserver Section. An atom of the ligand can also be restrained to a desired location as explained in the Restraints and Molecular Dynamics Section. The webserver outputs six docked conformations and corresponding AutoDock scores. Three of the six conformations are the conformations with the lowest AutoDock scores. The other three conformations are the representatives of the three largest clusters of the docked conformations.