Video Tutorials



  • A (typically large) ligand in PDB format
  • A protein receptor in PDB format
  • The coordinates of the center of the grid (i.e., the bounding box containing the binding site)
  • The dimensions of the grid (note that only atoms in the box are considered for the scoring)
  • Advanced options:
    • The number of conformers that are selected after each intermediate step of the incremental docking (which also defines the number of parallel threads)
    • The number of docking runs using the genetic algorithm (currently involved in AutoDock 4)
    • The size of the population maintained by the genetic algorithm


  • The three lowest-energy binding modes of the ligand as PDB files
  • The representatives of the three largest clusters of ligand conformations as PDB files
  • A text file containing the RMSD and energy values for the above results (dincresults.txt)
  • An interactive visualization for each result using the JSMol Viewer

Sample Results

DescriptionInput filesOutput
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

Molecule Preparation

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.

Receptor only:

  • remove water molecules
  • remove chains composed entirely of non-standard amino acids

Ligand and receptor:

  • remove lone pairs
  • add polar hydrogens and remove non-polar hydrogens
  • add Gasteiger charges

Grid Box

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.

Manual selection of grid box values with ADT. Autodocktools (ADT) is the ultimate GUI to set up, launch and analyze docking experiments with AutoDock 4. Using the “Grid” tab of ADT, the user can load the structure of the receptor and manually set up its location. After defining a proper grid box, the user can copy to DINC the three values corresponding to the size (number of grid points) and the three values corresponding to the center of the grid box (see video tutorial).