Difference between revisions of "2020 DOCK tutorial 3 with PDBID 4F4P"
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grid -i grid.in -o grid.out | grid -i grid.in -o grid.out | ||
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=V. Docking= | =V. Docking= | ||
Revision as of 13:37, 26 February 2020
This tutorial teaches you how to dock a drug molecule to a receptor.
/*This page is under construction*/
Contents
I. Introduction
DOCK
DOCK is an important molecular docking program in molecular modeling and drug design. It enables you to dock a small molecule (ligand) to a binding pocket of certain protein target (receptor) and find out correct binding geometry, types and number of interactions involve in binding and energies associate with binding. For this tutorial DOCK6.9 package was used. Purpose of using DOCK6.9 in this tutorial is to re-dock a ligand to a binding pocket of the receptor protein for pose reproduction and find out lead compounds which have stronger binding affinity with our receptor binding site.
Virtual Screening
This is a protocol widely used in drug design which enable you to find out small molecules that have higher binding affinity with the binding pocket of protein of interest by screening a millions of compounds in a virtual database (such as ZINC).
Organization of directories
Log in to the seawulf cluster and go to your group directory. Use following command to create files.
mkdir 001.files 002.surface_spheres 003.gridbox 004.dock 005.virtual_screen 006.virtual_screen_mpi 007.cartesianmin 008.rescore
4F4P
4F4P is the crystal structure of Tyrosine Kinase SYK in complex with ligand LASW836. You can get the pdb file from here [1]. The resolution is 2.37 Å. Click Download Files -> PDB Format to download PDB file.
II. Preparation of the ligand and receptor
Checking the structure
Read the article related to the PDB file [2] to understand protonation states, charges and other important information regarding the receptor and the ligand.
Open the pdb file through chimera and look at the structure.
Identify the main components of the model (receptor, ligand, solvent, cofactors). In our case, the PDB file contains one protein chain, ligand(OSB), sulfate ion(SO4(2-)) as a cofactor and water molecules (H2O).
Next, we are going to generate the receptor file and the ligand file.
Prepare the Receptor file
With the PDB file loaded by chimera, do Select -> Residue -> SO4 to select the sulfate. Use Actions -> Atoms/Bonds -> Delete to delete it. Then do Select -> Residue -> HOH to select the water molecules. Use the same method to delete it. Then do Select -> Structure -> (0SB) to select ligand molecule. Use the same method to delete it. Save the receptor as 4f4p_rec_noh.mol2.
OR
With the PDB file loaded by chimera, hold the control button and click on the protein chain to select a protein residue. Then click up arrow button to select the whole protein chain (Receptor). Then Select -> Invert(all models) to invert your selection (This will select all the components in your PDB file except receptor). Then do Actions->Atoms/bonds->Delete. You will remain with a protein receptor. Save the receptor as 4f4p_rec_noh.mol2.
Prepare the Ligand File
Open the pdf file again. Do Select -> Structure -> ligand(0SB) to select the ligand. Do Select -> Invert (all models), then delete the selected atoms. This will left the ligand molecule only. Save it as 4f4p_lig_noh.mol2.
Adding hydrogen and charge
Now we are going to add hydrogen atoms and charges to our receptor and ligand. Open 4f4p_rec_noh.mol2 file using Chimera and use the following instructions to prepare the receptor file to be used in DOCK. Tools -> Structure editing -> AddH. This command will add hydrogen to the receptor. Tools -> Structure editing -> Add Charge. This command will add charge to atoms to make the receptor neutral. Save the file as 4f4p_rec_h.mol2
Open 4f4p_lig_noh.mol2, follow the same steps for ligand file, add hydrogen. The Chimera added 2 hydrogens to the nitrogen where it is supposed to be only one, as referred in the pdb report. So remove one hydrogen.
(Hold Ctrl and select extra H, then Actions -> Atoms/Bonds -> delete.) (Therefore, Be really concern when adding Hydrogens using chimera since it is automatically adding unwanted hydrogen atoms. Compare your protonation state with PDB report and make sure you have correct structure after adding hydrogens.)
After removing hydrogen add charges to the ligand
Tools -> Structure editing -> Add Charge. After this save the file as 4f4p_lig_h.mol2.
copy the 4f4p_rec_h.mol2, 4f4p_rec_noh.mol2, 4f4p_lig_noh.mol2, 4f4p_lig_h.mol2 files in to 001.files directory
III. Generating receptor surface and spheres
Creating a surface (DMS) file
Open the 4f4p_rec_noh.mol2 file in chimera. Then Action -> surface -> show -> Shows the surface of the receptor without H.
Tools -> Structure editing -> write DMS -> name: 4f4p_rec_noh.dms -> This command saves the surface of the receptor in dms format.
copy the 4f4p_rec.dms file in to 002.surface_spheres directory.
Generating spheres
Go to 002.surface_spheres folder Create a new input file to create spheres by
vi INSPH
then type the following lines inside the file.
4f4p_rec_noh.dms R X 0.0 4.0 1.4 4f4p_rec.sph
The first line 4f4p_rec_noh.dms specifies the input file. R indicates that spheres generated will be outside of the receptor surface. X specifies all the points will be used. 0.0 is the distance in angstroms and it will avoid steric clashes. 4.0 is the maximum surface radius of the spheres and 1.4 is the minimum radius in angstroms.The last line 4f4p_rec.sph creates the sph file that contains clustered spheres.
Once the INSPH file is ready, type the following command to generate the spheres.
sphgen -i INSPH -o OUTSPH
Once sphgen command is successful, following output files will be created.
OUTSPH 4f4p_rec.sph
Open the f4p_rec.sph using Chimera along with 4f4p_rec_noh.mol2 file. You should get a similar output like the image below.
Selecting Spheres
Here we will be selecting the spheres which defines the binding pocket of the ligand because we are trying to direct the ligand towards that binding site rather than all over the receptor. To select the spheres type the following command.
sphere_selector 4f4p_rec.sph ../001.files/4f4p_noh_lig.mol2 10.0
This command will select all of the spheres within 10.0 angstroms of the ligand and output them to selected_spheres.sph.
Output files:
selected_spheres.sph
Visualize the selected spheres using Chimera to make sure the correct spheres are selected. Notice that, spheres around the ligand binding site are kept and all the other spheres are deleted by following sphere selector command .
IV. Generating box and grid
Generating box
Move to 003.gridbox directory Create a new file showbox.in and write the following lines in the file(# means comment ).
Y #Say 'Yes' to make a box 8.0 #The boundary of the box is at least 8 Angstroms from any spheres ../002.surface_spheres/selected_spheres.sph #The location and file name of the sphere file 1 #Use the first cluster of spheres (only 1 cluster in this case) 4f4p.box.pdb #The output filename
Use the following command to generate the box.
showbox < showbox.in
If this step is successful, you should see a new file (4f4p.box.pdb) in 003.gridbox folder.
Output file:
4f4p.box.pdb
Generating Grid
Create a new input file called grid.in and write the following information there.
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.files/4f4p_rec_h.mol2 box_file 4f4p.box.pdb vdw_definition_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn score_grid_prefix grid
save the file and run the following command.
grid -i grid.in -o grid.out
If this is successful, you will get following output files.
grid.out grid.nrg grid.bmp
V. Docking
Energy minimization
Before doing docking pose reproduction, energy minimization can be done in order to remove unfavorable intra-molecular clashes of the ligand. (If not it will affect the later steps of docking)
Go to 004.dock folder and open a file called min.in and type the following content there.
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file ../001.files/4f4p_lig_h.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol ../001.files/4f4p_lig_h.mol2 use_database_filter no orient_ligand no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../003.gridbox/grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no pharmacophore_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand yes simplex_max_iterations 1000 simplex_tors_premin_iterations 0 simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10.0 atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix 4f4p.lig.min write_orientations no num_scored_conformers 1 rank_ligands no
Save the file and run the following command. If you have done correctly, you will get a ouput file called 4f4p.lig.min__scored.mol2.
dock6 -i min.in -o min.out
Footprint Analysis
In order to see the minimized ligand compared to the original ligand through footprint analysis, open a file called footprint.in and type following.
conformer_search_type rigid use_internal_energy no ligand_atom_file 4f4p.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary no grid_score_secondary no multigrid_score_primary no multigrid_score_secondary no dock3.5_score_primary no dock3.5_score_secondary no continuous_score_primary no continuous_score_secondary no footprint_similarity_score_primary yes footprint_similarity_score_secondary no fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename ../001.files/4f4p_lig_h.mol2 fps_score_foot_compare_type Euclidean fps_score_normalize_foot no fps_score_foot_comp_all_residue yes fps_score_receptor_filename ../001.files/4f4p_rec_h.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 9 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0 pharmacophore_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix fps.min.output write_footprints yes write_hbonds yes write_orientations no num_scored_conformers 1 rank_ligands no
If dock runs successfully, you can find the following files generated
fps.min.output_footprint_scored.txt fps.min.output_hbond_scored.txt
In order to visualize the footprint, first we need to copy a python script into our directory, then run it:
cp /gpfs/projects/AMS536/zzz.programs/plot_footprint_single_magnitude.py ./ python plot_footprint_single_magnitude.py fps.min.output_footprint_scored.txt 50
A pdf document named fps.min.output_footprint_scored.txt.pdf will be generated. It looks like this:
Rigid Docking
Create an input file for rigid docking
touch rigid.in
Write lines below into the rigid.in
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 9 internal_energy_cutoff 100.0 ligand_atom_file ../001.files/4f4p_lig_h.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../001.files/4f4p_lig_h.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../002.surface_spheres/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../003.gridbox/grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no pharmacophore_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand yes simplex_max_iterations 1000 simplex_tors_premin_iterations 2 simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_random_seed 0 simplex_restraint_min no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix rigid.out write_orientations no num_scored_conformers 40 write_conformations yes cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
Run dock using the created input file.
dock6 -I rigid.in -o rigid.out
Once rigid docking is successful, you will get an output file. (rigid.out_scored.mol2) Visualize the output file using Chimera by following steps to check the rigid docking success.
Open Chimera File -> Open -> 4f4p_rec_h.mol2 (Actions -> Surface -> Show) File -> Open -> 4f4p_lig_h.mol2 Tools -> Surface/binding Analysis -> ViewDock -> Select the Rigid Dock output file. (rigid.out_scored.mol2) In the loaded dialog box select Dock4,5 or 6
Once everything is loaded go to the ViewDock window and use it's menu to view all the calculated properties regarding the rigid docked ligand by following the steps below.
Column -> Show -> Grid_Score Column -> Show -> HA_RMSDs
Follow the same steps to get all different properties as you interested.
You can choose different conformations from the ViewDock window. If you sorted it, the top one should be the conformation with lowest energy. Your visualized structure should be similar to the image below.
Fixed Anchor Docking
Create an input file called fad.in and use the following command.
dock6 -i fad.in
Use the following lines to answer the prompted questions as we did in rigid docking.
conformer_search_type flex write_fragment_libraries no user_specified_anchor no limit_max_anchors no min_anchor_size 5 pruning_use_clustering yes pruning_max_orients 1000 pruning_clustering_cutoff 100 pruning_conformer_score_cutoff 100.0 pruning_conformer_score_scaling_factor 1.0 use_clash_overlap no write_growth_tree no use_internal_energy yes internal_energy_rep_exp 9 internal_energy_cutoff 100.0 ligand_atom_file ../001.files/4f4p_lig_h.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../001.files/4f4p_lig_h.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../002.surface_spheres/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../003.gridbox/grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no pharmacophore_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand yes minimize_anchor yes minimize_flexible_growth yes use_advanced_simplex_parameters no simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_anchor_max_iterations 500 simplex_grow_max_iterations 500 simplex_grow_tors_premin_iterations 0 simplex_random_seed 0 simplex_restraint_min yes simplex_coefficient_restraint 10.0 atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix 4f4p_fad write_orientations no num_scored_conformers 40 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
Once docking is completed an output file will be generated. (4f4p_fad_scored.mol2) Follow the same method used in rigid docking to visualize the docked poses using Chimera. Once it is visualized, it should like the image below.
Flexible Docking
Create a new input file for flexible docking called flex.in and perform flexible docking using DOCK6 by following command.
dock6 -i flex.in
Answer the prompted questions using the following lines as we did in rigid and fixed anchor docking (or copy the following content in to flex.in file and save).
conformer_search_type flex user_specified_anchor no limit_max_anchors no min_anchor_size 5 pruning_use_clustering yes pruning_max_orients 1000 pruning_clustering_cutoff 100 pruning_conformer_score_cutoff 100.0 pruning_conformer_score_scaling_factor 1.0 use_clash_overlap no write_growth_tree no write_fragment_libraries no use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file 4f4p.lig.min_scored.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename 4f4p.lig.min_scored.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../002.surface_spheres/selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary yes grid_score_secondary no grid_score_rep_rad_scale 1 grid_score_vdw_scale 1 grid_score_es_scale 1 grid_score_grid_prefix ../003.boxgrid/grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no pharmacophore_score_secondary no descriptor_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no SASA_score_secondary no amber_score_secondary no minimize_ligand yes minimize_anchor yes minimize_flexible_growth yes use_advanced_simplex_parameters no simplex_max_cycles 1 simplex_score_converge 0.1 simplex_cycle_converge 1.0 simplex_trans_step 1.0 simplex_rot_step 0.1 simplex_tors_step 10.0 simplex_anchor_max_iterations 500 simplex_grow_max_iterations 500 simplex_grow_tors_premin_iterations 0 simplex_random_seed 0 simplex_restraint_min no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl ligand_outfile_prefix flex.out write_orientations no num_scored_conformers 1 rank_ligands no
Once flexible docking is completed an output mol2 file will be generated (flex.out_scored.mol2). Use the visualization steps used in rigid and fixed anchor docking and study the properties of the docking results.
