Video Tutorial


Usage

Descriptions of the inputs and outputs of the DINC webserver are provided below for reference.

Inputs:

  • A ligand (typically large) in PDB format
  • A protein receptor encoded in PDB format
  • Coordinates for the grid center
  • Dimensions of the grid
  • Advanced options:
    • Number of conformers to keep after each intermediate stage of incremental docking (also defines the number of parallel threads)
    • Number of GA runs (defines the number of serial docking runs using a genetic algorithm, currently AutoDock 4)
    • Population size (defines the pool of conformations used by the genetic algorithm)

Outputs:

  • Three complexes with the lowest energy conformations as PDB files
  • Representative complexes of all clustered dockings as PDB files
  • Text file containing RMSD + energy values for above the results (dincresults.txt)
  • An interactive visualization for each result using the JSMol Viewer

Sample Results

DescriptionInput filesOutput
1OHR ligand & receptor (Protease inhibitor, drug, 12 DoFs) ligand, receptor results page
1SKJ ligand & receptor (SH2 domain inhibitor, peptidomimetic, 17 DoFs) ligand, receptor results page
4D0D ligand & receptor (MHC binder, peptide, 26 DoFs) ligand, receptor results page

Grid Box

The grid box defines the volume that will be 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 will be considered by the scoring function during the energy computation; the interaction energies will be pre-computed for a probe atom at the grid positions 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, the user will need to use a proper graphical interface such as autodocktools (ADT) or available plugins for popular visualization tools. Additional information and tools can be found in 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).