Difference between revisions of "2024 DOCK tutorial 3 with PDBID 1Y0X"
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=Box and Grid Generation= | =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=== | ===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=== | ===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: | ||
+ | #grid.bmp | ||
+ | #grid.nrg | ||
+ | #1y0xGridInfo.out | ||
+ | |||
+ | in your directory. With the box and grid successfully generated we are ready to move onto the energy minimization step. | ||
=Energy Minimization= | =Energy Minimization= |
Revision as of 22:31, 17 March 2024
Contents
- 1 Introduction
- 2 Preparation of the ligand and protein
- 3 Creating the Protein Binding Site Surface
- 4 Box and Grid Generation
- 5 Energy Minimization
- 6 DOCK
- 7 Virtual Screening of a Ligand Library
- 8 Cartesian Minimization of Virtually Screened Small Molecules
- 9 Rescoring and Ranking Virtually Screened Molecules
Introduction
- Setting up your environment
- Downloading a protein from the PDB database
- Determining if there are any missing loops in the structure and if they need to be modeled
- Preparing the ligand
- Preparing the protein
- Finding the binding site of the protein
Learning Objectives
Setting Up Your Environment
Downloading a protein from the PDB database
Preparation of the ligand and protein
- Evaluate the structure to determine if there are any missing loops
- Prepare the protein structure
- Prepare the ligand structure
Evaluating the Structure
- Select an atom at near the start of the missing section (hold the ctrl button while clicking it)
- Select another atom near the binding site (hold ctrl + shift while clicking the second atom)
- Go to Tools → Structure Analysis → Distances
Preparing the Protein file
- Select an atom on the protein
- Press the up arrow until the entire protein is selected
- Go to Select → Invert (all models). This will change the selection from the protein to everything else in the structure
- Go to Actions → Atoms/Bonds → Delete
- Save the structure with a new file name (i.e. 4s0v_protein_only.pdb). Your pdb file will now look similar to this:
- Adding hydrogens
- Adding charge
- Click on one atom anywhere on the protein
- Click on Select → Zone. This will cause the following dialogue box to appear:
Preparing the Ligand File
- Select an atom on the ligand
- Press the up arrow until the entire ligand is selected (you may have to press the up arrow many times)
- Go to Select → Invert (all models). This will change the selection from the ligand to everything else in the structure
- Go to Actions → Atom/Bonds → Delete
- Save the structure with a new file name (i.e. 4s0v_ligand_only.pdb). The image will look similar to this:
- Add hydrogens
- Add charges
Final Steps
Creating the Protein Binding Site Surface
Creating the Required Surface (DMS) File
Generating Spheres for the Binding Site
Binding Site Spheres
- scp selected_spheres.sph to your local computer
- Close any open sessions you have in Chimera
- In Chimera open selected_spheres.sph
- In the current session, open the original protein/ligand complex (4s0v.pdb)
- You should see the spheres located within the binding site of the protein, similar to:
- Hold down ctrl and click on a sphere
- Press the up arrow until all spheres are selected
- Actions → Atoms/Bonds → hide
- 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:
- grid.bmp
- grid.nrg
- 1y0xGridInfo.out
in your directory. With the box and grid successfully generated we are ready to move onto the energy minimization step.