Difference between revisions of "2023 DOCK tutorial 3 with PDBID 2P16"

Revision as of 12:02, 14 March 2023

Introduction

Needs to be updated

DOCK

Needs to be updated

2P16 System

Needs to be updated

Directory Preparation

Protein and Ligand Preparation

Protein Preparation

Ligand Preparation

Surface Spheres Generation

Grid Box

Grid Generation

Box Generation

Ligand Minimization

Footprint Analysis

DOCKING

The goal of docking in this tutorial is to reproduce the crystal structure from x-ray diffraction. This is called “pose reproduction”; this can be used to validate the docking software and parameters of use within the software. If the pose reproduction is not successful, it might be possible that: 1.the parameters to dock the ligand needs to be changed, 2.preparation of ligand or receptor went wrong, 3.the system itself is not suitable to reproduce in the software. Having a preliminary docking pose before getting into virtual screening–a procedure docking thousands of molecules–would be helpful to validate the results you will get in the future. In DOCK6 (at the point of 2020), the docking is successful if the RMSD of the docked pose is within 2.0Å from the crystal pose. In this section, we will be working on (i)rigid docking, (ii)flexible docking, (iii)fixed anchor docking.

Rigid Docking

Rigid docking does not conduct pose searching with dihedral rotations or bond length perturbations. It takes 3 translational and 3 rotational degrees of freedom to do its pose searching. Therefore, rigid docking is less computationally expensive compared to flex docking. Since we already have the crystal structure of the ligand bound at the active site, it is expected to have a good reproduction using rigid docking.

The first step is to create an input file by rigid.in

Insert the following into that file: <>

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100
ligand_atom_file                                             2p16.ligand.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                                      2p16.ligand.min_scored.mol2
use_database_filter                                          no
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           selected_spheres.sph
max_orientations                                             2000
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                                       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                                        no
atom_model                                                   all
vdw_defn_file                                              
/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               
/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex.defn
flex_drive_file                                              
/gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex_drive.tbl
ligand_outfile_prefix                                        rigid.out
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

</>

Make sure to (i)have all the files you need (selected_spheres.sph and 2p16.ligand.min_scored.mol2) and (ii)inputs are correct.

Run the input file with the following command: <>

dock6 -i rigid.in -o rigid.out

</>

After the job is complete, you should see a file named “rigid.out_scored.mol2”. This is the output that shows the docked poses (if you rank it, it will show from the highest to lowest docking score). If you open the file, in the first part, you will see general information about the docked pose including the grid scores. Make sure that the output file is not empty. The pose can be visualized using Chimera. After you load the protein you prepared (simply open the file), you can go to: Tools -> Surface/Binding Analysis -> ViewDock -> *choose the file* -> Dock4,5, or 6. Along with the visualized pose, you will see a small window popping out with the quantitative information as you saw in the first part of the output file. Since we took a crystal structure of the ligand, minimized, and rigidly docked into the same protein, it is expected that the produced pose is well-reproduced. If you want to check the reproducibility, you could check out the RMSD (root-mean-square-deviation) values for the pose.

Fixed Anchor Docking

As it is said “fixed anchor” docking, this is a docking method that docks while maintaining the orientation of the initially placed structure. For this reason, “comformer_search_type” is flexible, while “write orientation” is turned off. This allows more flexibility in its conformational change compared to rigid docking methods while maintaining the general placement. You can also pick specific fragments within the molecules to be the anchor.

Not to mess up the outputs with other types of docking methods, make a new folder by <> mkdir anchor_dock </>

In this directory, create an input file:

<>

vi fixed.in

</>

Insert the following: <> 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 10000 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 12 internal_energy_cutoff 100.0 ligand_atom_file 2p16.charge.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol yes rmsd_reference_filename 2p16.charge.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 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 simplex_trans_step 1 simplex_rot_step 0.1 simplex_tors_step 10 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/dock6.10/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex_drive.tbl ligand_outfile_prefix 2P16_fixed write_orientations no num_scored_conformers 1 rank_ligands no </>

Start the docking by: <>

dock6 -i fixed.in -o fixed.out

</>

The resulting docked pose:

RMSD: 0.9235 Å relative to the minimized crystal pose

The RMSD in this case is still small, and within the cutoff, but slightly larger than the rigid docking which is also evident in the image. It makes sense that the pose generated from fixed anchor docking is not as close to the crystal pose since we allowed the algorithm to explore different rotational conformations, increasing the likelihood of generating a new conformation.

Flex Docking

Finally, flex docking is a docking method that allows flexibility in the rotatable bonds in the ligand and orientation of the compound. This method has the largest exploration of the pose for the ligand, although the calculation time takes the longest. To speed up the calculation time, it is necessary to use cpus provided in seawulf. To use the cpus, we need to submit our run to the queue.

Create a directory: <> mkdir flex_dock </>

First, start with creating an input file, flex.in. <> 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 5000 pruning_clustering_cutoff 2500 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 12 internal_energy_cutoff 100.0 ligand_atom_file ../Rigid_dock/2p16.ligand.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 ../Rigid_dock/2p16.ligand.min_scored.mol2 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file ../Rigid_dock/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 ../Rigid_dock/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/dock6.10/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/flex_drive.tbl ligand_outfile_prefix flex.out write_orientations yes num_scored_conformers 10 write_conformations yes cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no

Now that we have our .in file, we need to make a slurm script to run it. To make a script, first run the following:

<>

 vi flex.sh

</>

Inside of this file, copy-paste the following:

<>

 #!/bin/bash
 #SBATCH --time=10:00:00
 #SBATCH --nodes=1
 #SBATCH --ntasks=28
 #SBATCH --job-name=2p16_flex_dock
 #SBATCH --output=2p16_flex_dock
 #SBATCH -p long-28core

 dock6 -i flex.in -o 2p16_flex.out

</>

You can submit the queue by <> sbatch flex.in </>

Once complete, you will see three .mol2 files: (1)flex.out_scored.mol2: best poses scored from the highest to lowest (2)flex.out_conformers.mol2: poses with all conformations of the ligand (3)flex.out_orients.mol2: poses with all orientations of the ligand

To check the best pose, check the flex.out_scored.mol2. You can open it on Chimera using viewdock. Compare with the crystal structure - is the pose with freedom of orientation and rotatable bonds matching with the binding pose in real life?