2024 DOCK tutorial 3 with PDBID 1Y0X

Introduction

1. Setting up your environment
2. Downloading a protein from the PDB database
3. Determining if there are any missing loops in the structure and if they need to be modeled
4. Preparing the ligand
5. Preparing the protein
6. Finding the binding site of the protein

Preparation of the ligand and protein

1. Evaluate the structure to determine if there are any missing loops
2. Prepare the protein structure
3. Prepare the ligand structure

Evaluating the Structure

1. Select an atom at near the start of the missing section (hold the ctrl button while clicking it)
2. Select another atom near the binding site (hold ctrl + shift while clicking the second atom)
3. Go to Tools → Structure Analysis → Distances

Preparing the Protein file

1. Select an atom on the protein
2. Press the up arrow until the entire protein is selected
3. Go to Select → Invert (all models). This will change the selection from the protein to everything else in the structure
4. Go to Actions → Atoms/Bonds → Delete
5. Save the structure with a new file name (i.e. 4s0v_protein_only.pdb). Your pdb file will now look similar to this:
6. Adding hydrogens
7. Adding charge
8. Click on one atom anywhere on the protein
9. Click on Select → Zone. This will cause the following dialogue box to appear:

Preparing the Ligand File

1. Select an atom on the ligand
2. Press the up arrow until the entire ligand is selected (you may have to press the up arrow many times)
3. Go to Select → Invert (all models). This will change the selection from the ligand to everything else in the structure
4. Go to Actions → Atom/Bonds → Delete
5. Save the structure with a new file name (i.e. 4s0v_ligand_only.pdb). The image will look similar to this:

1. Add hydrogens
2. Add charges

Creating the Protein Binding Site Surface

Binding Site Spheres

1. scp selected_spheres.sph to your local computer
2. Close any open sessions you have in Chimera
3. In Chimera open selected_spheres.sph
4. In the current session, open the original protein/ligand complex (4s0v.pdb)
5. You should see the spheres located within the binding site of the protein, similar to:

1. Hold down ctrl and click on a sphere
2. Press the up arrow until all spheres are selected
3. Actions → Atoms/Bonds → hide
4. Verify the ligand is where the spheres were

Box and Grid Generation

The next step in the docking process is to generate energy interactions between the atoms of the protein and ligand. If this was done for the whole complex it would take too long to run to be useful. To get around this computationally expensive step, dock uses a box/grid method. We will define a box around the area of interest for the protein/ligand and DOCK will generate a grid within this box which will be used in the energy calculations.

Generating the Box

To generate the box we will be working again on the command line using a DOCK program called showbox. Start by logging into Seawulf and navigating to your 003.gridbox directory. We need to make a new file called showbox.in by typing:

   vi showbox.in

This will create a new file, with a filename of showbox.in and open it in vi. The following commands need to be typed:

     Y
     8.0 
     ../002.surface_spheres/selected_spheres.sph
     1 
     1y0x.box.pdb

Remember to change the last line to be a filename with the number of protein you are working with. The second line of this code (8.0) is telling dock how many angstroms from the selected spheres to draw the box. Depending on your system you may need to modify this number.

To run this file, simply type:

    showbox < showbox.in

If showbox was successful the file 1y0x.box.pdb will now be in your directory.

Generating the Grid

Now that we have our box defined we need to instruct DOCK to generate the grid within it. We do this using a DOCK program called grid:

  vi grid.in

This command will generate and open a file named grid.in. The commands to be typed into this file are:

  allow_non_integral_charges                no
  compute_grids                             yes
  grid_spacing                              0.4
  output_molecule                           no
  contact_score                             no
  energy_score                              yes
  energy_cutoff_distance                    9999
  atom_model                                a
  attractive_exponent                       6
  repulsive_exponent                        9
  distance_dielectric                       yes
  dielectric_factor                         4.
  bump_filter                               yes
  bump_overlap                              0.75
  receptor_file                              ../001.structure/protein_final.mol2
  box_file                                  1y0x.box.pdb
  vdw_definition_file                       /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn
  score_grid_prefix                         grid

The only change you need to make to the above commands is the receptor_file and box_file to reflect the files you previously generated.

Once this file is saved, run it:

   grid -i grid.in -o 1y0xGridInfo.out

Be patient, this step might take a few minutes to run. You will know it's worked successfully if you see:

1. grid.bmp
2. grid.nrg
3. 1y0xGridInfo.out

in your directory. With the box and grid successfully generated we are ready to move onto the energy minimization step.