|1OHR protein & ligand (Protease inhibitor, drug, 10 DoFs)||ligand, receptor||results page|
|1SKJ protein & ligand (SH2 domain inhibitor, peptidomimetic, 15 DoFs)||ligand, receptor||results page|
|4D0D protein & ligand (MHC binder, peptide, 26 DoFs)||ligand, receptor||results page|
As part of its pre-processing steps, DINC automatically performs a number of repair and cleanup operations on the receptor and ligand provided as input.
The binding box defines the volume that is considered for ligand sampling; it should include the receptor's binding cleft and be large enough to accommodate the ligand. The binding box also defines which atoms of the receptor are considered by the scoring function when computing binding energies. Therefore, the location and dimensions of the binding box should depend on the receptor's structure and its orientation in the input file. To find appropriate values, you should use a proper graphical interface, such as AutoDockTools (ADT), or available plugins for molecular visualization tools. Additional resources can be found at the links below.