Difference between revisions of "2021 Denovo tutorial 3 with PDBID 1S19"

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 +
This tutorial continues where we left off from the virtual screening of 1S19, a structure of the vitamin D nuclear receptor bound to the side chain analogue calcipotriol.
 +
 
= Focused Denovo Design with PDB 1S19 =
 
= Focused Denovo Design with PDB 1S19 =
  
−
This tutorial assumes that you have already completed the tutorial for the Virtual Screen of 1S19 (found [https://ringo.ams.stonybrook.edu/index.php/2021_DOCK_tutorial_3_with_PDBID_1S19 here]). Some of the output files genrated from that tutorial will be required for this denovo tutorial of 1S19.
+
In this section, we will generate new ligand structures using a fragment library. It will require the use of some of the output files from the Virtual Screen tutorial (found [https://ringo.ams.stonybrook.edu/index.php/2021_DOCK_tutorial_3_with_PDBID_1S19 here]).
 +
 
 +
===Fragment Libraries===
 +
 
 +
We will use a focused fragment library file based on the original ligand. To begin, we will create a new directory for this.
 +
 
 +
mkdir fraglib
 +
 
 +
Create a new file called '''fragment.in''' with the following inputs.
 +
 
 +
conformer_search_type                                        flex
 +
write_fragment_libraries                                    yes
 +
fragment_library_prefix                                      fraglib
 +
fragment_library_freq_cutoff                                1
 +
fragment_library_sort_method                                freq
 +
fragment_library_trans_origin                                no
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
ligand_atom_file                                            ../001_structure/1s19_ligand_dockprep.mol2
 +
limit_max_ligands                                            no
 +
skip_molecule                                                no
 +
read_mol_solvation                                          no
 +
calculate_rmsd                                              no
 +
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                                              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                                        fragment.out
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 
 +
To run this, type:
 +
 
 +
dock6 -i fragment.in -o fragment.out
 +
 
 +
Once this has ran, the following files should have been generated:
 +
'''fraglib_linker.mol2, fraglib_rigid.mol2, fraglib_scaffold.mol2, fraglib_sidechain.mol2, fraglib_torenv.dat'''. To check the number of fragments in each file, you can type:
 +
 
 +
grep -wc MOLECULE *.mol2
 +
 
 +
You should get the following output upon using this command:
 +
 
 +
fraglib_linker.mol2:4
 +
fraglib_rigid.mol2:0
 +
fraglib_scaffold.mol2:2
 +
fraglib_sidechain.mol2:2
 +
  fragment.out_scored.mol2:0
 +
 
 +
 
 +
These fragments can also be visualized in Chimera. The results are shown below.
  
−
===Fregment Libraries===
+
[[File:frag_three.png|thumb|center|500px|2p16 fragments. The left image is the side chain fragments, the center are the scaffold fragments and the right image is the linker fragment.]]
  
 
===Focused Denovo Growth===
 
===Focused Denovo Growth===
 +
 +
We will be using the fragments that we have generated for the denovo dock. The different fragments will be connected together using restraints such as molecular weight and formal charges. DOCK will check the torsion environment file that was created in the fragment generation section to ensure reasonable connections are being made.
 +
 +
To begin, we will make a new directory and call it denovo_focus
 +
 +
mkdir dn_focus
 +
 +
Create a file called '''focus.in''' and copy the following script into the file.
 +
 +
conformer_search_type                                        denovo
 +
dn_fraglib_scaffold_file                                    ../fraglib/fraglib_scaffold.mol2
 +
dn_fraglib_linker_file                                      ../fraglib/fraglib_linker.mol2
 +
dn_fraglib_sidechain_file                                    ../fraglib/fraglib_sidechain.mol2
 +
dn_user_specified_anchor                                    no
 +
dn_use_torenv_table                                          yes
 +
dn_torenv_table                                              ../fraglib/fraglib_torenv.dat
 +
dn_sampling_method                                          graph
 +
dn_graph_max_picks                                          30
 +
dn_graph_breadth                                            3
 +
dn_graph_depth                                              2
 +
dn_graph_temperature                                        100.0
 +
dn_pruning_conformer_score_cutoff                            100.0
 +
dn_pruning_conformer_score_scaling_factor                    1.0
 +
dn_pruning_clustering_cutoff                                100.0
 +
dn_constraint_mol_wt                                        550.0
 +
dn_constraint_rot_bon                                        15
 +
dn_constraint_formal_charge                                  2.0
 +
dn_heur_unmatched_num                                        1
 +
dn_heur_matched_rmsd                                        2.0
 +
dn_unique_anchors                                            1
 +
dn_max_grow_layers                                          9
 +
dn_max_root_size                                            25
 +
dn_max_layer_size                                            25
 +
dn_max_current_aps                                          5
 +
dn_max_scaffolds_per_layer                                  1
 +
dn_write_checkpoints                                        yes
 +
dn_write_prune_dump                                          no
 +
dn_write_orients                                            no
 +
dn_write_growth_trees                                        no
 +
dn_output_prefix                                            dn_focus.out
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
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                                        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
  
 
===Focused Denovo Rescore===
 
===Focused Denovo Rescore===
 +
 +
Now that all of the ligands have been generated in silico, we will want to rescore them based on their binding properties to predict which ones would be the best binders in vitro.
 +
 +
First, create a new directory and dock6 input file:
 +
 +
mkdir 12.dn_focus_rescore
 +
touch dn_rescore.in
 +
 +
Define parameters in the dn_rescore.in file as follows and submit the job:
 +
 +
conformer_search_type                                        rigid
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
ligand_atom_file                                            ../dn_focus/dn_focus.out.denovo_build.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                          no
 +
footprint_similarity_score_secondary                        no
 +
pharmacophore_score_primary                                  no
 +
pharmacophore_score_secondary                                no
 +
descriptor_score_primary                                    yes
 +
descriptor_score_secondary                                  no
 +
descriptor_use_grid_score                                    no
 +
descriptor_use_multigrid_score                              no
 +
descriptor_use_continuous_score                              no
 +
descriptor_use_footprint_similarity                          yes
 +
descriptor_use_pharmacophore_score                          yes
 +
descriptor_use_tanimoto                                      yes
 +
descriptor_use_hungarian                                    yes
 +
descriptor_use_volume_overlap                                yes
 +
descriptor_fps_score_use_footprint_reference_mol2            yes
 +
descriptor_fps_score_footprint_reference_mol2_filename      ../004.dock/1s19.lig.min_scored.mol2
 +
descriptor_fps_score_foot_compare_type                      Euclidean
 +
descriptor_fps_score_normalize_foot                          no
 +
descriptor_fps_score_foot_comp_all_residue                  yes
 +
descriptor_fps_score_receptor_filename                      ../001.structure/1s19.dockprep.mol2
 +
descriptor_fps_score_vdw_att_exp                            6
 +
descriptor_fps_score_vdw_rep_exp                            12
 +
descriptor_fps_score_vdw_rep_rad_scale                      1
 +
descriptor_fps_score_use_distance_dependent_dielectric      yes
 +
descriptor_fps_score_dielectric                              4.0
 +
descriptor_fps_score_vdw_fp_scale                            1
 +
descriptor_fps_score_es_fp_scale                            1
 +
descriptor_fps_score_hb_fp_scale                            0
 +
descriptor_fms_score_use_ref_mol2                            yes
 +
descriptor_fms_score_ref_mol2_filename                      ../004.dock/1s19.lig.min_scored.mol2
 +
descriptor_fms_score_write_reference_pharmacophore_mol2      no
 +
descriptor_fms_score_write_reference_pharmacophore_txt      no
 +
descriptor_fms_score_write_candidate_pharmacophore          no
 +
descriptor_fms_score_write_matched_pharmacophore            no
 +
descriptor_fms_score_compare_type                            overlap
 +
descriptor_fms_score_full_match                              yes
 +
descriptor_fms_score_match_rate_weight                      5.0
 +
descriptor_fms_score_match_dist_cutoff                      1.0
 +
descriptor_fms_score_match_proj_cutoff                      0.7071
 +
descriptor_fms_score_max_score                              20
 +
descriptor_fingerprint_ref_filename                          ../004.dock/1s19_lig.min_scored.mol2
 +
descriptor_hms_score_ref_filename                            ../004.dock/1s19_lig.min_scored.mol2
 +
descriptor_hms_score_matching_coeff                          -5
 +
descriptor_hms_score_rmsd_coeff                              1
 +
descriptor_volume_score_reference_mol2_filename              ../004.dock/1s19.lig.min_scored.mol2
 +
descriptor_volume_score_overlap_compute_method              analytical
 +
descriptor_weight_fps_score                                  1
 +
descriptor_weight_pharmacophore_score                        1
 +
descriptor_weight_fingerprint_tanimoto                      -1
 +
descriptor_weight_hms_score                                  1
 +
descriptor_weight_volume_overlap_score                      -1
 +
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
 +
chem_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/chem.defn
 +
pharmacophore_defn_file                                     
 +
/gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/ph4.defn
 +
ligand_outfile_prefix                                        descriptor.output
 +
write_footprints                                            yes
 +
write_hbonds                                                yes
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 +
dock6 -i dn_rescore.in -o dn_rescore.out
 +
 +
It may be helpful to submit this job using a slurm script. An example is shown below:
 +
 +
#!/bin/bash
 +
#SBATCH --time=48:00:00
 +
#SBATCH --nodes=1
 +
#SBATCH --ntasks=28
 +
#SBATCH --job-name=dn_rescore
 +
#SBATCH --output=dn_rescore.out
 +
#SBATCH -p long-28core
 +
 +
cd $SLURM_SUBMIT_DIR
 +
echo "starting Dock6.9 simulation"
 +
/gpfs/projects/AMS536/zzz.programs/dock6.9_release/bin/dock6.mpi -i dn_rescore.in -o dn_rescore.out
  
 
= Generic Denovo Design with PDB 1S19 =
 
= Generic Denovo Design with PDB 1S19 =
 +
 +
With focused docking, we only used fragments from the original ligand. With generic docking, we instead using a library of fragments and linkers to make new ligands. We will use the following input:
 +
 +
mkdir 13_dn_generic_denovo
 +
touch gn_denovo.in
 +
dock6 -i gn_denovo.in
 +
 +
conformer_search_type                                        denovo
 +
dn_fraglib_scaffold_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_scaffold.mol2
 +
dn_fraglib_linker_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_linker.mol2
 +
dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_sidechain.mol2
 +
dn_user_specified_anchor                                    no
 +
dn_use_torenv_table                                          yes
 +
dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_torenv.dat
 +
dn_sampling_method                                          graph
 +
dn_graph_max_picks                                          30
 +
dn_graph_breadth                                            3
 +
dn_graph_depth                                              2
 +
dn_graph_temperature                                        100
 +
dn_pruning_conformer_score_cutoff                            100
 +
dn_pruning_conformer_score_scaling_factor                    1.0
 +
dn_pruning_clustering_cutoff                                100.0
 +
dn_constraint_mol_wt                                        550.0
 +
dn_constraint_rot_bon                                        15
 +
dn_constraint_formal_charge                                  2.0
 +
dn_heur_unmatched_num                                        1
 +
dn_heur_matched_rmsd                                        2.0
 +
dn_unique_anchors                                            1
 +
dn_max_grow_layers                                          9
 +
dn_max_root_size                                            25
 +
dn_max_layer_size                                            25
 +
dn_max_current_aps                                          5
 +
dn_max_scaffolds_per_layer                                  1
 +
dn_write_checkpoints                                        yes
 +
dn_write_prune_dump                                          no
 +
dn_write_orients                                            no
 +
dn_write_growth_trees                                        no
 +
dn_output_prefix                                            gn_denovo_output
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
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                                          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                          no
 +
footprint_similarity_score_secondary                        no
 +
pharmacophore_score_primary                                  no
 +
pharmacophore_score_secondary                                no
 +
descriptor_score_primary                                    yes
 +
descriptor_score_secondary                                  no
 +
descriptor_use_grid_score                                    yes
 +
descriptor_use_pharmacophore_score                          no
 +
descriptor_use_tanimoto                                      no
 +
descriptor_use_hungarian                                    no
 +
descriptor_use_volume_overlap                                no
 +
descriptor_grid_score_rep_rad_scale                          1
 +
descriptor_grid_score_vdw_scale                              1
 +
descriptor_grid_score_es_scale                              1
 +
descriptor_grid_score_grid_prefix                            ../003.gridbox/grid
 +
descriptor_weight_grid_score                                1
 +
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
 +
 +
If we look at our output file gn_denovo.out, we see that 60285 molecules were processed in 2478 seconds using SLURM. You can visualize these molecules  and their corresponding binding interactions using ViewDock in Chimera as before.

Latest revision as of 15:24, 15 March 2021

This tutorial continues where we left off from the virtual screening of 1S19, a structure of the vitamin D nuclear receptor bound to the side chain analogue calcipotriol.

Focused Denovo Design with PDB 1S19

In this section, we will generate new ligand structures using a fragment library. It will require the use of some of the output files from the Virtual Screen tutorial (found here).

Fragment Libraries

We will use a focused fragment library file based on the original ligand. To begin, we will create a new directory for this. 

mkdir fraglib

Create a new file called fragment.in with the following inputs. 

conformer_search_type                                        flex
write_fragment_libraries                                     yes
fragment_library_prefix                                      fraglib
fragment_library_freq_cutoff                                 1
fragment_library_sort_method                                 freq
fragment_library_trans_origin                                no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../001_structure/1s19_ligand_dockprep.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
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                                              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                                        fragment.out
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

To run this, type: 

dock6 -i fragment.in -o fragment.out

Once this has ran, the following files should have been generated: fraglib_linker.mol2, fraglib_rigid.mol2, fraglib_scaffold.mol2, fraglib_sidechain.mol2, fraglib_torenv.dat. To check the number of fragments in each file, you can type: 

grep -wc MOLECULE *.mol2

You should get the following output upon using this command: 

fraglib_linker.mol2:4
fraglib_rigid.mol2:0
fraglib_scaffold.mol2:2
fraglib_sidechain.mol2:2
fragment.out_scored.mol2:0


These fragments can also be visualized in Chimera. The results are shown below.

2p16 fragments. The left image is the side chain fragments, the center are the scaffold fragments and the right image is the linker fragment.

Focused Denovo Growth

We will be using the fragments that we have generated for the denovo dock. The different fragments will be connected together using restraints such as molecular weight and formal charges. DOCK will check the torsion environment file that was created in the fragment generation section to ensure reasonable connections are being made.

To begin, we will make a new directory and call it denovo_focus 

mkdir dn_focus

Create a file called focus.in and copy the following script into the file. 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     ../fraglib/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       ../fraglib/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    ../fraglib/fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              ../fraglib/fraglib_torenv.dat
dn_sampling_method                                           graph
dn_graph_max_picks                                           30
dn_graph_breadth                                             3
dn_graph_depth                                               2
dn_graph_temperature                                         100.0
dn_pruning_conformer_score_cutoff                            100.0
dn_pruning_conformer_score_scaling_factor                    1.0
dn_pruning_clustering_cutoff                                 100.0
dn_constraint_mol_wt                                         550.0
dn_constraint_rot_bon                                        15
dn_constraint_formal_charge                                  2.0
dn_heur_unmatched_num                                        1
dn_heur_matched_rmsd                                         2.0
dn_unique_anchors                                            1
dn_max_grow_layers                                           9
dn_max_root_size                                             25
dn_max_layer_size                                            25
dn_max_current_aps                                           5
dn_max_scaffolds_per_layer                                   1
dn_write_checkpoints                                         yes
dn_write_prune_dump                                          no
dn_write_orients                                             no
dn_write_growth_trees                                        no
dn_output_prefix                                             dn_focus.out
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
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                                        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

Focused Denovo Rescore

Now that all of the ligands have been generated in silico, we will want to rescore them based on their binding properties to predict which ones would be the best binders in vitro.

First, create a new directory and dock6 input file: 

mkdir 12.dn_focus_rescore
touch dn_rescore.in

Define parameters in the dn_rescore.in file as follows and submit the job: 

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../dn_focus/dn_focus.out.denovo_build.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                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    no
descriptor_use_multigrid_score                               no
descriptor_use_continuous_score                              no
descriptor_use_footprint_similarity                          yes
descriptor_use_pharmacophore_score                           yes
descriptor_use_tanimoto                                      yes
descriptor_use_hungarian                                     yes
descriptor_use_volume_overlap                                yes
descriptor_fps_score_use_footprint_reference_mol2            yes
descriptor_fps_score_footprint_reference_mol2_filename       ../004.dock/1s19.lig.min_scored.mol2
descriptor_fps_score_foot_compare_type                       Euclidean
descriptor_fps_score_normalize_foot                          no
descriptor_fps_score_foot_comp_all_residue                   yes
descriptor_fps_score_receptor_filename                       ../001.structure/1s19.dockprep.mol2
descriptor_fps_score_vdw_att_exp                             6
descriptor_fps_score_vdw_rep_exp                             12
descriptor_fps_score_vdw_rep_rad_scale                       1
descriptor_fps_score_use_distance_dependent_dielectric       yes
descriptor_fps_score_dielectric                              4.0
descriptor_fps_score_vdw_fp_scale                            1
descriptor_fps_score_es_fp_scale                             1
descriptor_fps_score_hb_fp_scale                             0
descriptor_fms_score_use_ref_mol2                            yes
descriptor_fms_score_ref_mol2_filename                       ../004.dock/1s19.lig.min_scored.mol2
descriptor_fms_score_write_reference_pharmacophore_mol2      no
descriptor_fms_score_write_reference_pharmacophore_txt       no
descriptor_fms_score_write_candidate_pharmacophore           no
descriptor_fms_score_write_matched_pharmacophore             no
descriptor_fms_score_compare_type                            overlap
descriptor_fms_score_full_match                              yes
descriptor_fms_score_match_rate_weight                       5.0
descriptor_fms_score_match_dist_cutoff                       1.0
descriptor_fms_score_match_proj_cutoff                       0.7071
descriptor_fms_score_max_score                               20
descriptor_fingerprint_ref_filename                          ../004.dock/1s19_lig.min_scored.mol2
descriptor_hms_score_ref_filename                            ../004.dock/1s19_lig.min_scored.mol2
descriptor_hms_score_matching_coeff                          -5
descriptor_hms_score_rmsd_coeff                              1
descriptor_volume_score_reference_mol2_filename              ../004.dock/1s19.lig.min_scored.mol2
descriptor_volume_score_overlap_compute_method               analytical
descriptor_weight_fps_score                                  1
descriptor_weight_pharmacophore_score                        1
descriptor_weight_fingerprint_tanimoto                       -1
descriptor_weight_hms_score                                  1
descriptor_weight_volume_overlap_score                       -1
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
chem_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/chem.defn
pharmacophore_defn_file                                       
/gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/ph4.defn
ligand_outfile_prefix                                        descriptor.output
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

dock6 -i dn_rescore.in -o dn_rescore.out

It may be helpful to submit this job using a slurm script. An example is shown below: 

#!/bin/bash
#SBATCH --time=48:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=28
#SBATCH --job-name=dn_rescore
#SBATCH --output=dn_rescore.out
#SBATCH -p long-28core

cd $SLURM_SUBMIT_DIR
echo "starting Dock6.9 simulation"
/gpfs/projects/AMS536/zzz.programs/dock6.9_release/bin/dock6.mpi -i dn_rescore.in -o dn_rescore.out

Generic Denovo Design with PDB 1S19

With focused docking, we only used fragments from the original ligand. With generic docking, we instead using a library of fragments and linkers to make new ligands. We will use the following input: 

mkdir 13_dn_generic_denovo
touch gn_denovo.in
dock6 -i gn_denovo.in

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/fraglib_torenv.dat
dn_sampling_method                                           graph
dn_graph_max_picks                                           30
dn_graph_breadth                                             3
dn_graph_depth                                               2
dn_graph_temperature                                         100
dn_pruning_conformer_score_cutoff                            100
dn_pruning_conformer_score_scaling_factor                    1.0
dn_pruning_clustering_cutoff                                 100.0
dn_constraint_mol_wt                                         550.0
dn_constraint_rot_bon                                        15
dn_constraint_formal_charge                                  2.0
dn_heur_unmatched_num                                        1
dn_heur_matched_rmsd                                         2.0
dn_unique_anchors                                            1
dn_max_grow_layers                                           9
dn_max_root_size                                             25
dn_max_layer_size                                            25
dn_max_current_aps                                           5
dn_max_scaffolds_per_layer                                   1
dn_write_checkpoints                                         yes
dn_write_prune_dump                                          no
dn_write_orients                                             no
dn_write_growth_trees                                        no
dn_output_prefix                                             gn_denovo_output
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
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                                           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                           no
footprint_similarity_score_secondary                         no
pharmacophore_score_primary                                  no
pharmacophore_score_secondary                                no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
descriptor_use_grid_score                                    yes
descriptor_use_pharmacophore_score                           no
descriptor_use_tanimoto                                      no
descriptor_use_hungarian                                     no
descriptor_use_volume_overlap                                no
descriptor_grid_score_rep_rad_scale                          1
descriptor_grid_score_vdw_scale                              1
descriptor_grid_score_es_scale                               1
descriptor_grid_score_grid_prefix                            ../003.gridbox/grid
descriptor_weight_grid_score                                 1
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

If we look at our output file gn_denovo.out, we see that 60285 molecules were processed in 2478 seconds using SLURM. You can visualize these molecules and their corresponding binding interactions using ViewDock in Chimera as before.

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