2017 DOCK tutorial 2 with PDB 3GPL NEW
For additional Rizzo Lab tutorials see DOCK Tutorials. Use this link Wiki Formatting as a reference for editing the wiki. This tutorial was developed collaboratively by a subsection of the AMS 536 class of 2017, using DOCK v6.8.
- 1 I. Introduction
- 2 II. Preparing the Receptor and Ligand
- 3 III. Generating Receptor Surface and Spheres
- 4 IV. Generating Box and Grid
- 5 V. Docking a Single Molecule for Pose Reproduction
- 6 VI. Virtual Screening
- 7 VIII. Frequently Encountered Problems
DOCK is a molecular docking program used in drug discovery. It was developed by Irwin D. Kuntz, Jr. and colleagues at UCSF (see UCSF DOCK). This program, given a protein binding site and a small molecule, tries to predict the correct binding mode of the small molecule in the binding site, and the associated binding energy. Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug. DOCK works well as a screening procedure for generating leads, but is not currently as useful for optimization of those leads.
DOCK 6 uses an incremental construction algorithm called anchor and grow. It is described by a three-step process:
- Rigid portion of ligand (anchor) is docked by geometric methods.
- Non-rigid segments added in layers; energy minimized.
- The resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations.
In this tutorial we will use PDB code 3PGL, the deposited crystal structure of Scp1 in complex with rabeprazole.
While performing docking, it is convenient to adopt a standard directory structure / naming scheme, so that files are easy to find / identify.For this tutorial, we will use something similar to the following:
~username/AMS536-Spring2016/dock-tutorial/00.files/ /01.dockprep/ /02.surface-spheres/ /03.box-grid/ /04.dock/ /05.large-virtual-screen/ /06.virtual-screen/ /07.footprint/ /08.print_fps
In addition, most of the important files that are derived from the original crystal structure will be given a prefix that is the same as the PDB code, '3pgl'. The following sections in this tutorial will adhere to this directory structure/naming scheme.
II. Preparing the Receptor and Ligand
Download the PDB file (3PGL) and move file 3PGL.pdb to 00.files
3PGL.pdb was copied to raw_3pgl.pdb with command
cp 3PGL.pdb raw_3pgl.pdb
raw_3pgl.pdb was opened with VI terminal editor
The header information, connect records, and waters were deleted. Change HETATM to ATOM, and delete all rows that have B in the fifth column
Change RZX A to LIG B to make the ligand a different chain
Prepare ligand and receptor files for dock
Create dockprep file
Open raw_3pgl.pdb file in chimera, in Tools, find structure editing, then click AddH to add hydrogen in this system.
Also in structure editing, click Add charge, then, changing AMBER ff14SB to AMBER ff99SB and changing net charge to +2.
Save it as 3pgl.dockprep.mol2 in 01.dockprep.
Create receptor file
Open 3pgl.dockprep.mol2 in chimera, then click Select, Chain, B to choose ligand. Click Actions, Atom/Bonds, Delete and save the molecule as 3pgl.rec.mol2 in 01.dockprep.
Create ligand file
Open 3pgl.dockprep.mol2 in chimera, using the same method delete the protein molecule. Save this as 3pgl.lig.mol2 in 01.dockprep.
Create no hydrogen receptor file
Open 3pgl.rec.mol2 in chimera, click Select, Chemistry, H and then delete using Actions, Atoms/Bonds, Delete.
Save this as 3pgl.rec.noH.pdb in 01.dockprep.
III. Generating Receptor Surface and Spheres
Change directory to 02.surface-sphere Open 3pgl.rec.noH.pdb in Chimera
To generate the molecular surface:
Action --> Surface --> Show
Save the .dms file
Tools --> Structure editing --> write DMS
.dms save to 3pgl.rec.noH.dms
Create surface spheres
create input file INSPH
3pgl.rec.noH.dms R X 0.0 4.0 1.4 3pgl.rec.sph
line 1 designates input file line 2 designates the generated spheres will be outside the receptor surface line 3 designates that all points on the receptor will be used line 4 designates the maximum surface radius of the spheres line 5 designates the minimum surface radius of the spheres line 6 designates the output file name
sphgen -i INSPH -o OUTSPH
sphgen is the sphere generation program from dock -i desginates the input file: INSPH -o designates the output file
At this point it is beneficial to visualize the spheres that were created. This can be done with chimera: Open chimera from the terminal choose file --> open 4qmz.rec.mol2 choose file --> open 4qmz.rec.sph
The image that appears should resemble this:
Then we need to select the spheres pertinent to our docking experiment. Usually these speheres will be the closest N spheres to the native ligand molecule.
sphere_selector 3pgl.rec.sph ../01.dockprep/3pgl.lig.mol2 8.0
This command will select all of the spheres within 8.0 angstroms of the ligand and output them to selected_spheres.sph
To visualize the spheres using Chimera as previously done: Launch Chimera, choose File -> Open, choose 3pgl.rec.noH.pdb File -> Open, choose output_spheres_selected.pdb Select -> Residue -> SPH Actions -> Atoms/Bonds -> sphere The selected spheres with the receptor surface should look similar to that as seen below:
IV. Generating Box and Grid
enter directory 03.box-grid
create input showbox.in
Y 8.0 ../02.surface-spheres/selected_spheres.sph 1 3pgl.box.pdb
This input designates to dock that: we want to create a box the box length should be 8.0 Angstroms use the selected spheres in the file desginated output the box to the file specified
to use this input type:
showbox < showbox.in
This box can be visualized in chimera using a similar approach as visualizing the spheres
Compute the energy grid
create grid.in file using
When prpmped, answer the questions as follows:
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 12 distance_dielectric yes dielectric_factor 4 bump_filter yes bump_overlap 0.75 receptor_file ../01.dockprep/3pgl.rec.mol2 box_file ../03.box-grid/3pgl.box.pdb vdw_definition_file /opt/AMS536/dock6/parameters/vdw_AMBER_parm99.defn score_grid_prefix grid
this script should output verbosely to the terminal and produce 2 output files, grid.bmp and grid.nrg, both binary files.
V. Docking a Single Molecule for Pose Reproduction
create min.in file and run dock with this as the input
touch min.in dock6 -i min.in
When prompted, answer the questions as follows:
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file ../../01.dockprep/3pgl.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../01.dockprep/3pgl.lig.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 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 yes continuous_score_secondary no cont_score_rec_filename ../01.dockprep/3pgl.rec.mol2 cont_score_att_exp 6 cont_score_rep_exp 12 cont_score_rep_rad_scale 1 cont_score_use_dist_dep_dielectric yes cont_score_dielectric 4.0 cont_score_vdw_scale 1 cont_score_es_scale 1 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 no atom_model all vdw_defn_file /opt/AMS536/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /opt/AMS536/dock6/parameters/flex.defn flex_drive_file /opt/AMS536/dock6/parameters/flex_drive.tbl ligand_outfile_prefix 3pgl.min write_orientations no num_scored_conformers 1 rank_ligands no
this command will output 3pgl.lig.min_scored.mol2
This structure can be visualized using chimera and loading the surface into chimera along with the minimized and unminimized ligand structures:
At this point we are going to calculate the van der wals and electrostatic footprints for the unminimized and minimized ligand structures in relation to the receptor active site.
create the input file: footprint.in
conformer_search_type rigid use_internal_energy no ligand_atom_file ../3pgl.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_use_footprint_reference_mol2 yes fps_footprint_reference_mol2_filename ../01.dockprep/3pgl.lig.mol2 fps_foot_compare_type Euclidean fps_normalize_foot no fps_foot_comp_all_residue yes fps_receptor_filename ../01.dockprep/3pgl.rec.mol2 fps_vdw_att_exp 6 fps_vdw_rep_exp 12 fps_vdw_rep_rad_scale 1 fps_use_distance_dependent_dielectric yes fps_dielectric 4.0 fps_vdw_fp_scale 1 fps_es_fp_scale 1 fps_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 /opt/AMS536/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /opt/AMS536/dock6/parameters/flex.defn flex_drive_file /opt/AMS536/dock6/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
this footprint calculation can be run in the same way as the minimization:
dock6 -i footprint.in
This will output three files: fps.min.output_scored.mol2
With an in house script, plot_footprint_single_magnitude.py the two sets of footprints will be plotted for comparison
this script will be run using:
python plot_footprint_single_magnitude.py fps.min.output_scored_footprint_scored.txt 50
The output will look something like this:
To run rigid docking, create rigid.in file and run dock with it as an input, use commands
touch rigid.in dock6 -i rigid.in
And answer the prompts as follows
conformer_search_type rigid use_internal_energy yes internal_energy_rep_exp 12 internal_energy_cutoff 100.0 ligand_atom_file ../../01.dockprep/3pgl.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename ../../01.dockprep/3pgl.lig.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../02.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 ../03.box-grid/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 /opt/AMS536/dock6/parameters/vdw_AMBER_parm99.defn flex_defn_file /opt/AMS536/dock6/parameters/flex.defn flex_drive_file /opt/AMS536/dock6/parameters/flex_drive.tbl ligand_outfile_prefix 3pgl_rigid_restraint write_orientations no num_scored_conformers 40 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no