Difference between revisions of "2024 Denovo tutorial 3 with PDBID 1Y0X"

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(Created page with "=Introduction= Continuing from Virtual Screening tutorial, we have the De Novo design tutorial. De Novo means from the beginning, thus, in this tutorial, we are learning to d...")
 
 
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Creating new directories in your workspace like the similar:
 
Creating new directories in your workspace like the similar:
  
−
 
+
[[File: 1y0xdir1.png|center]]
  
 
=De Novo Refinement=
 
=De Novo Refinement=
Line 25: Line 25:
 
==Running De Novo Refinement==
 
==Running De Novo Refinement==
 
Locate to 012 directory and scp the .mol2 file into the directory. Make an input file for DOCK with the following input:
 
Locate to 012 directory and scp the .mol2 file into the directory. Make an input file for DOCK with the following input:
 +
  conformer_search_type                                        denovo
 +
  dn_fraglib_scaffold_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_scaffold.mol2
 +
  dn_fraglib_linker_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_linker.mol2
 +
  dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_sidechain.mol2
 +
  dn_user_specified_anchor                                    yes
 +
  dn_fraglib_anchor_file                                      ligand_dummy.mol2
 +
  dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_torenv.dat
 +
  dn_name_identifier                                          1y0x_denovo
 +
  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                    2.0
 +
  dn_pruning_clustering_cutoff                                100.0
 +
  dn_mol_wt_cutoff_type                                        soft
 +
  dn_upper_constraint_mol_wt                                  1000.0
 +
  dn_lower_constraint_mol_wt                                  0.0
 +
  dn_mol_wt_std_dev                                            35.0
 +
  dn_constraint_rot_bon                                        15
 +
  dn_constraint_formal_charge                                  5
 +
  dn_heur_unmatched_num                                        1
 +
  dn_heur_matched_rmsd                                        2.0
 +
  dn_unique_anchors                                            1
 +
  dn_max_grow_layers                                          1
 +
  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                                            denovo_output
 +
  use_internal_energy                                          yes
 +
  internal_energy_rep_exp                                      12
 +
  internal_energy_cutoff                                      100.0
 +
  use_database_filter                                          no
 +
  orient_ligand                                                no
 +
  bump_filter                                                  no
 +
  score_molecules                                              yes
 +
  contact_score_primary                                        no
 +
  grid_score_primary                                          yes
 +
  grid_score_rep_rad_scale                                    1
 +
  grid_score_vdw_scale                                        1
 +
  grid_score_es_scale                                          1
 +
  grid_score_grid_prefix                                      ../003.gridbox/grid
 +
  minimize_ligand                                              yes
 +
  minimize_anchor                                              no
 +
  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_grow_max_iterations                                  250
 +
  simplex_grow_tors_premin_iterations                          0
 +
  simplex_random_seed                                          0
 +
  simplex_restraint_min                                        yes
 +
  simplex_coefficient_restraint                                10
 +
  atom_model                                                  all
 +
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_de_novo.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
 +
 +
Run the Refinement by command:
 +
  dock6 -i denovo.in -o denovo.out
 +
Once the job has completed you will see the following new files in your directory:
 +
#denovo_output.anchor_1.root_layer_1.mol2
 +
#denovo_output.denovo_build.mol2
 +
#denovo.out
 +
 +
Opening the _build.mol2 molecule in Chimera using View Dock tool to look at the newly refined molecule.
 +
 +
=Focused De Novo Design
 +
In focused De Novo, a chemical group from our compound is selected as an anchor and the anchor can be sampled against the protein to find the most attractive position within the binding site. From there, the molecule is grown back from the anchor.
 +
 +
==Fragment Library Generation==
 +
This is the library of chemical group fragments that dock will use as binding blocks to regrow the molecule. In this case, focused de novo design use only the fragments from the original ligand.
 +
Locate to your 013a. directory and create an input file using the following input:
 +
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/H_charged_ligand.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/dock6.10/parameters/vdw_de_novo.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                                        focused
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
write_conformations                                          no
 +
cluster_conformations                                        yes
 +
cluster_rmsd_threshold                                      2.0
 +
rank_ligands                                                no
 +
 +
And run the input file using command:
 +
dock6 -i focused.in -o focused.out
 +
 +
Once the program has successfully run you'll see the following new files in your directory:
 +
 +
#focused_scored.mol2
 +
#fragLib_linker.mol2
 +
#fragLib_rigid.mol2
 +
#fragLib_scaffold.mol2
 +
#fragLib_sidechain.mol2
 +
#fragLib_torenv.dat
 +
 +
==De Novo Design==
 +
After constructing the fragment library, we can perform focused De Novo Design to grow the molecule. The input is as followed:
 +
conformer_search_type                                        denovo
 +
dn_fraglib_scaffold_file                                    ../013a.fragLib/fragLib_scaffold.mol2
 +
dn_fraglib_linker_file                                      ../013a.fragLib/fragLib_linker.mol2
 +
dn_fraglib_sidechain_file                                    ../013a.fragLib/fragLib_sidechain.mol2
 +
dn_user_specified_anchor                                    no
 +
dn_use_torenv_table                                          yes
 +
dn_torenv_table                                              ../013a.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                                            2
 +
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                                        yes
 +
dn_output_prefix                                            focused
 +
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/dock6.10/parameters/vdw_de_novo.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
 +
 +
And execute the docking using the command:
 +
dock6 -i focus.in -o focus.out
 +
 +
Once the run is done, you can see new files with the newly built molecules. The most important file is the
 +
focused.denovo_build.mol2
 +
 +
==Rescoring Designed Molecules==
 +
The molecules built can be then rescored to be compared against the crystallographic ligand in terms of interaction energy values. We can do that using the input file as followed:
 +
conformer_search_type                                        rigid
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
ligand_atom_file                                            ../013b.focusGrowth/focused.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.energy_min/protein.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/H_charged_protein.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.energy_min/protein.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.energy_min/protein.lig.min_scored.mol2
 +
descriptor_hms_score_ref_filename                            ../004.energy_min/protein.lig.min_scored.mol2
 +
descriptor_hms_score_matching_coeff                          -5
 +
descriptor_hms_score_rmsd_coeff                              1
 +
descriptor_volume_score_reference_mol2_filename              ../004.energy_min/protein.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/dock6.10/parameters/vdw_de_novo.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
 +
chem_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/chem.defn
 +
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/ph4.defn
 +
ligand_outfile_prefix                                        focus_rescore
 +
write_footprints                                            yes
 +
write_hbonds                                                yes
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 +
And execute the rescoring using the command:
 +
dock6 -i rescore.in -o rescore.out
 +
 +
You will see the output contains 3 files:
 +
#focus_rescore_footprint_scored.txt
 +
#focus_rescore_hbond_scored.txt
 +
#focus_rescore_scored.mol2
 +
 +
If we compare the best scoring molecule with the energy minimized ligand, the differences are minimal.
 +
 +
=Generic De Novo Design=
 +
 +
This type of algorithm performs the same kind of anchored fragment growth as observed in focused De Novo with the only difference of using the premade fragment library that contains various common fragments in thousands of drug molecules.
 +
After locating to 014. directory, you can use the input file as follow to carry out this docking:
 +
conformer_search_type                                        denovo
 +
dn_fraglib_scaffold_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_scaffold.mol2
 +
dn_fraglib_linker_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_linker.mol2
 +
dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_sidechain.mol2
 +
dn_user_specified_anchor                                    no
 +
dn_use_torenv_table                                          yes
 +
dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.10/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                                            genericDenovo_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/dock6.10/parameters/vdw_de_novo.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
 +
 +
Since the process may take long, it is a good idea to submit this job to the cluster using the script as followed:
 +
 +
#!/bin/bash
 +
#
 +
#SBATCH --job-name=genericLib
 +
#SBATCH --output=genericLib_output.txt
 +
#SBATCH --ntasks-per-node=28
 +
#SBATCH --nodes=4
 +
#SBATCH --time=48:00:00
 +
#SBATCH -p long-28core
 +
 +
mpirun -np 112 dock6 -i generic.in -o generic.out
 +
 +
The most important file in the result is genericDenovo_output.denovo_build.mol2, which can be viewed in Chimera using View Dock.
 +
You can check how many molecules were built using the command:
 +
grep MOLECULE 4s0v_genericDenovo_output.denovo_build.mol2 | wc -l
 +
 +
You can compare the grid score as well as other interacting energy values to determine if generic De Novo Docking has provided better binding molecules than the crystallographic ligand.

Latest revision as of 11:13, 8 May 2024

Introduction

Continuing from Virtual Screening tutorial, we have the De Novo design tutorial. De Novo means from the beginning, thus, in this tutorial, we are learning to design the molecule that can bind to our protein from scratch. There are 3 different algorithms for the De Novo Design:

  1. Generic DeNovo Design
  2. Focused Fragment Design
  3. DeNovo Refinement

Setting Up Your Environment

Creating new directories in your workspace like the similar:

1y0xdir1.png

De Novo Refinement

This algorithm allows us to refine an existing molecule by deleting part of the molecule and let DOCK6 decide what chemical group can be regrow from the deleted area to fit with the protein pocket. Hear is how you can perform it:

Set up your dummy atom

  1. Open the protein and ligand in chimera
  2. Choose a chemical group inside the binding pocket that you want to delete
  3. Get the name of the first atom connecting the chemical group to the rest of the compound by placing the mouse on top of the structure
  4. Delete all other atoms after that first atom that you located
  5. Save the .mol2 file of the ligand and open it in a text editor program
  6. Change the name of the Atom to "DU1" and the atom type to "Du"
  7. Save the .mol2 file again

Running De Novo Refinement

Locate to 012 directory and scp the .mol2 file into the directory. Make an input file for DOCK with the following input: 

 conformer_search_type                                        denovo
 dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_scaffold.mol2
 dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_linker.mol2
 dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_sidechain.mol2
 dn_user_specified_anchor                                     yes
 dn_fraglib_anchor_file                                       ligand_dummy.mol2
 dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_torenv.dat
 dn_name_identifier                                           1y0x_denovo
 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                    2.0
 dn_pruning_clustering_cutoff                                 100.0
 dn_mol_wt_cutoff_type                                        soft
 dn_upper_constraint_mol_wt                                   1000.0
 dn_lower_constraint_mol_wt                                   0.0
 dn_mol_wt_std_dev                                            35.0
 dn_constraint_rot_bon                                        15
 dn_constraint_formal_charge                                  5
 dn_heur_unmatched_num                                        1
 dn_heur_matched_rmsd                                         2.0
 dn_unique_anchors                                            1
 dn_max_grow_layers                                           1
 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                                             denovo_output
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 use_database_filter                                          no
 orient_ligand                                                no
 bump_filter                                                  no
 score_molecules                                              yes
 contact_score_primary                                        no
 grid_score_primary                                           yes
 grid_score_rep_rad_scale                                     1
 grid_score_vdw_scale                                         1
 grid_score_es_scale                                          1
 grid_score_grid_prefix                                       ../003.gridbox/grid
 minimize_ligand                                              yes
 minimize_anchor                                              no
 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_grow_max_iterations                                  250
 simplex_grow_tors_premin_iterations                          0
 simplex_random_seed                                          0
 simplex_restraint_min                                        yes
 simplex_coefficient_restraint                                10
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/vdw_de_novo.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

Run the Refinement by command: 

 dock6 -i denovo.in -o denovo.out

Once the job has completed you will see the following new files in your directory:

  1. denovo_output.anchor_1.root_layer_1.mol2
  2. denovo_output.denovo_build.mol2
  3. denovo.out

Opening the _build.mol2 molecule in Chimera using View Dock tool to look at the newly refined molecule.

=Focused De Novo Design In focused De Novo, a chemical group from our compound is selected as an anchor and the anchor can be sampled against the protein to find the most attractive position within the binding site. From there, the molecule is grown back from the anchor.

Fragment Library Generation

This is the library of chemical group fragments that dock will use as binding blocks to regrow the molecule. In this case, focused de novo design use only the fragments from the original ligand. Locate to your 013a. directory and create an input file using the following input: 

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/H_charged_ligand.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/dock6.10/parameters/vdw_de_novo.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                                        focused
write_orientations                                           no
num_scored_conformers                                        1
write_conformations                                          no
cluster_conformations                                        yes
cluster_rmsd_threshold                                       2.0
rank_ligands                                                 no

And run the input file using command: 

dock6 -i focused.in -o focused.out

Once the program has successfully run you'll see the following new files in your directory:

  1. focused_scored.mol2
  2. fragLib_linker.mol2
  3. fragLib_rigid.mol2
  4. fragLib_scaffold.mol2
  5. fragLib_sidechain.mol2
  6. fragLib_torenv.dat

De Novo Design

After constructing the fragment library, we can perform focused De Novo Design to grow the molecule. The input is as followed: 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     ../013a.fragLib/fragLib_scaffold.mol2
dn_fraglib_linker_file                                       ../013a.fragLib/fragLib_linker.mol2
dn_fraglib_sidechain_file                                    ../013a.fragLib/fragLib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              ../013a.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                                            2
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                                        yes
dn_output_prefix                                             focused
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/dock6.10/parameters/vdw_de_novo.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

And execute the docking using the command: 

dock6 -i focus.in -o focus.out

Once the run is done, you can see new files with the newly built molecules. The most important file is the 

focused.denovo_build.mol2

Rescoring Designed Molecules

The molecules built can be then rescored to be compared against the crystallographic ligand in terms of interaction energy values. We can do that using the input file as followed: 

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../013b.focusGrowth/focused.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.energy_min/protein.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/H_charged_protein.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.energy_min/protein.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.energy_min/protein.lig.min_scored.mol2
descriptor_hms_score_ref_filename                            ../004.energy_min/protein.lig.min_scored.mol2
descriptor_hms_score_matching_coeff                          -5
descriptor_hms_score_rmsd_coeff                              1
descriptor_volume_score_reference_mol2_filename              ../004.energy_min/protein.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/dock6.10/parameters/vdw_de_novo.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
chem_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/chem.defn
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/ph4.defn
ligand_outfile_prefix                                        focus_rescore
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

And execute the rescoring using the command: 

dock6 -i rescore.in -o rescore.out

You will see the output contains 3 files:

  1. focus_rescore_footprint_scored.txt
  2. focus_rescore_hbond_scored.txt
  3. focus_rescore_scored.mol2

If we compare the best scoring molecule with the energy minimized ligand, the differences are minimal.

Generic De Novo Design

This type of algorithm performs the same kind of anchored fragment growth as observed in focused De Novo with the only difference of using the premade fragment library that contains various common fragments in thousands of drug molecules. After locating to 014. directory, you can use the input file as follow to carry out this docking: 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    /gpfs/projects/AMS536/zzz.programs/dock6.10/parameters/fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              /gpfs/projects/AMS536/zzz.programs/dock6.10/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                                             genericDenovo_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/dock6.10/parameters/vdw_de_novo.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

Since the process may take long, it is a good idea to submit this job to the cluster using the script as followed: 

#!/bin/bash
#
#SBATCH --job-name=genericLib
#SBATCH --output=genericLib_output.txt
#SBATCH --ntasks-per-node=28
#SBATCH --nodes=4
#SBATCH --time=48:00:00
#SBATCH -p long-28core

mpirun -np 112 dock6 -i generic.in -o generic.out

The most important file in the result is genericDenovo_output.denovo_build.mol2, which can be viewed in Chimera using View Dock. You can check how many molecules were built using the command: 

grep MOLECULE 4s0v_genericDenovo_output.denovo_build.mol2 | wc -l

You can compare the grid score as well as other interacting energy values to determine if generic De Novo Docking has provided better binding molecules than the crystallographic ligand.

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