|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 grid box defines the volume that is considered for ligand sampling; it should include the receptor's binding cleft, and it should be large enough to acommodate the ligand. The grid box also defines which atoms of the receptor are considered by the scoring function during the energy computation; the interaction energies are pre-computed for a probe atom at the grid points within this box. Therefore, the position and dimensions of the grid box depend on the specific receptor and on the orientation of the structure in the input file. To find appropriate values, users have to use a proper graphical interface such as autodocktools (ADT) or available plugins for popular visualization tools. Additional information can be found at the links below.