Difference between revisions of "2019 Denovo design tutorial 1 with PDB 2BXF"

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(Created page with "==De novo design with PDB 1C87 focused fragment library== ===Preparing The Files=== First of all, we need to create a directory for the fragment library. mkdir fraglib Mov...")
 
(Undo revision 12724 by Stonybrook (talk))
 
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−
==De novo design with PDB 1C87 focused fragment library==
+
=='''I.'' de-novo'' design with PDB 2BXF (Focused)'''==
  
−
===Preparing The Files===
+
===Fragment Libraries===
−
First of all, we need to create a directory for the fragment library.
+
A focused fragment library will be used in this tutorial, in order to attempt building the same ligand. A focused fragment library can be generated using the same ligand.  
  
 +
Create a new directory for the fragment library.
 
  mkdir fraglib
 
  mkdir fraglib
  
−
Move to fraglib directory and create an input file, ''fraglib.in''
+
Inside the fraglib directory create a new input file for fragment generation.
 +
touch fraglib.in
  
 +
Generate the fragments by calling the input file through DOCK6
 +
dock6 -i fraglib.in
 +
 +
Answer the prompted questions interactively using the following lines.
 
  conformer_search_type                                        flex
 
  conformer_search_type                                        flex
 
  write_fragment_libraries                                    yes
 
  write_fragment_libraries                                    yes
Line 13: Line 19:
 
  fragment_library_freq_cutoff                                1
 
  fragment_library_freq_cutoff                                1
 
  fragment_library_sort_method                                freq
 
  fragment_library_sort_method                                freq
−
  fragment_library_trans_origin                                no  
+
  fragment_library_trans_origin                                no
−
  use_internal_energy                                          no
+
  use_internal_energy                                          yes
−
  ligand_atom_file                                            /gpfs/projects/AMS536/2018/seung/001.files/lig_withH_charge_1c87.mol2
+
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
  ligand_atom_file                                            /Path_to_file/2BXF_lig_withH.mol2
 
  limit_max_ligands                                            no
 
  limit_max_ligands                                            no
 
  skip_molecule                                                no
 
  skip_molecule                                                no
 
  read_mol_solvation                                          no
 
  read_mol_solvation                                          no
−
  calculate_rmsd                                              no  
+
  calculate_rmsd                                              no
 
  use_database_filter                                          no
 
  use_database_filter                                          no
−
  orient_ligand                                                no
+
  orient_ligand                                                yes
 +
automated_matching                                          yes
 +
receptor_site_file                                          /Path_to_file/selected_spheres.sph
 +
max_orientations                                            1000
 +
critical_points                                              no
 +
chemical_matching                                            no
 +
use_ligand_spheres                                          no
 
  bump_filter                                                  no
 
  bump_filter                                                  no
 
  score_molecules                                              no
 
  score_molecules                                              no
Line 28: Line 42:
 
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
−
  ligand_outfile_prefix                                        fraglib
+
  ligand_outfile_prefix                                        output
 
  write_orientations                                          no
 
  write_orientations                                          no
 
  num_scored_conformers                                        1
 
  num_scored_conformers                                        1
 
  rank_ligands                                                no
 
  rank_ligands                                                no
  
−
fraglib_linker.mol2, fraglib_rigid.mol2, fraglib_scaffold.mol2, fraglib_scored.mol2, fraglib_sidechain.mol2 and  fraglib_torenv.dat will be created.         
+
Once fragment generation is completed, following files will be generated. (fraglib_linker.mol2, fraglib_rigid.mol2, fraglib_scaffold.mol2, fraglib_sidechain.mol2, fraglib_torenv.dat) Open the mol2 files using chimera and check if the fragments match with the ligand used for fragment generation.
−
You can check how many linkers and side chains are in your system.
 
−
[seshin@login fraglib]$ grep -wc MOLECULE fraglib_linker.mol2 
 
−
3
 
−
[seshin@login fraglib]$ grep -wc MOLECULE fraglib_sidechain.mol2  
 
−
1
 
−
There are 3 linkers and 1 side chain.                                               
 
−
Once fraglib output files are created, make''denovo.in'' input file and run it interactively.  
 
  
−
  conformer_search_type                                        denovo  
+
[[File:Sidechain.jpg|thumb|center|300px|2BXF sidechain fragment]]
−
  dn_fraglib_scaffold_file                                    fraglib_scaffold.mol2
+
 
−
  dn_fraglib_linker_file                                      fraglib_linker.mol2  
+
===Focused Denovo Growth===
−
  dn_fraglib_sidechain_file                                    fraglib_sidechain.mol2
+
The generated fragments will be used to perform the de novo dock. Here the fragments will added together restricted by different properties like maximum layers, formal charge and molecular weight. Before each connection, DOCK will check with the torsion environment file created in frgment generation to see if that particular connection is seen before. If not the connection won't be made.
−
  dn_user_specified_anchor                                    yes
+
 
−
dn_fraglib_anchor_file                                      anchor1.mol2
+
Create a new directory for denovo dock.
 +
mkdir denovo
 +
 
 +
Create a new input file for denovo dock.
 +
touch denovo.in
 +
 
 +
Run the input file through dock.
 +
dock6 -i denovo.in
 +
 
 +
Answer the prompted question interactively using the following lines.
 +
 
 +
conformer_search_type                                        denovo
 +
  conformer_search_type                                        denovo
 +
  dn_fraglib_scaffold_file                                    /8.fraglib/fraglib_scaffold.mol2
 +
  dn_fraglib_linker_file                                      /8.fraglib/fraglib_linker.mol2
 +
  dn_fraglib_sidechain_file                                    /8.fraglib/fraglib_sidechain.mol2
 +
  dn_user_specified_anchor                                    no
 
  dn_use_torenv_table                                          yes
 
  dn_use_torenv_table                                          yes
−
  dn_torenv_table                                              fraglib_torenv.dat
+
  dn_torenv_table                                              /8.fraglib/fraglib_torenv.dat
 
  dn_sampling_method                                          graph
 
  dn_sampling_method                                          graph
 
  dn_graph_max_picks                                          30
 
  dn_graph_max_picks                                          30
Line 56: Line 79:
 
  dn_graph_temperature                                        100.0
 
  dn_graph_temperature                                        100.0
 
  dn_pruning_conformer_score_cutoff                            100.0
 
  dn_pruning_conformer_score_cutoff                            100.0
−
  dn_pruning_conformer_score_scaling_factor                    2.0
+
  dn_pruning_conformer_score_scaling_factor                    1.0
 
  dn_pruning_clustering_cutoff                                100.0
 
  dn_pruning_clustering_cutoff                                100.0
 
  dn_constraint_mol_wt                                        550.0
 
  dn_constraint_mol_wt                                        550.0
Line 63: Line 86:
 
  dn_heur_unmatched_num                                        1
 
  dn_heur_unmatched_num                                        1
 
  dn_heur_matched_rmsd                                        2.0
 
  dn_heur_matched_rmsd                                        2.0
−
  dn_unique_anchors                                            4
+
  dn_unique_anchors                                            2
 
  dn_max_grow_layers                                          9
 
  dn_max_grow_layers                                          9
 
  dn_max_root_size                                            25
 
  dn_max_root_size                                            25
Line 70: Line 93:
 
  dn_max_scaffolds_per_layer                                  1
 
  dn_max_scaffolds_per_layer                                  1
 
  dn_write_checkpoints                                        yes
 
  dn_write_checkpoints                                        yes
−
  dn_write_prune_dump                                          yes
+
  dn_write_prune_dump                                          no
 
  dn_write_orients                                            no
 
  dn_write_orients                                            no
−
  dn_write_growth_trees                                        no
+
  dn_write_growth_trees                                        yes
−
  dn_output_prefix                                            1c87.final
+
  dn_output_prefix                                            2BXF.final
 
  use_internal_energy                                          yes
 
  use_internal_energy                                          yes
 
  internal_energy_rep_exp                                      12
 
  internal_energy_rep_exp                                      12
−
  internal_energy_cutoff                                      100.0  
+
  internal_energy_cutoff                                      100.0
 
  use_database_filter                                          no
 
  use_database_filter                                          no
 
  orient_ligand                                                yes
 
  orient_ligand                                                yes
 
  automated_matching                                          yes
 
  automated_matching                                          yes
−
  receptor_site_file                                          ../../002.spheres/selected_spheres.sph
+
  receptor_site_file                                          /2.surface_spheres/selected_spheres.sph
 
  max_orientations                                            1000
 
  max_orientations                                            1000
 
  critical_points                                              no
 
  critical_points                                              no
Line 94: Line 117:
 
  grid_score_vdw_scale                                        1
 
  grid_score_vdw_scale                                        1
 
  grid_score_es_scale                                          1
 
  grid_score_es_scale                                          1
−
  grid_score_grid_prefix                                      ../../004.grid/grid
+
  grid_score_grid_prefix                                      /3.boxgrid/grid
 
  multigrid_score_secondary                                    no
 
  multigrid_score_secondary                                    no
 
  dock3.5_score_secondary                                      no
 
  dock3.5_score_secondary                                      no
Line 119: Line 142:
 
  simplex_grow_tors_premin_iterations                          0
 
  simplex_grow_tors_premin_iterations                          0
 
  simplex_random_seed                                          0
 
  simplex_random_seed                                          0
−
  simplex_restraint_min                                        no  
+
  simplex_restraint_min                                        no
 
  atom_model                                                  all
 
  atom_model                                                  all
 
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
 
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
Line 125: Line 148:
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
  
−
Create ''vi submit.sh'' in order to submit a job to create the output file.
+
[[File:Denovo rescored.jpg|thumb|center|600px|2BXF growthed molecules]]
−
#!/bin/bash
+
 
−
#PBS -l walltime=48:00:00
+
===Focused Denovo Rescore===
−
#PBS -l nodes=1:ppn=24
+
 
−
#PBS -N 1c87_denovo
+
Create a new directory
−
#PBS -V
+
  mkdir focuseddenovorescore
−
#PBS -q long
+
 
−
  echo "Job started on"
+
Copy your reference .mol2 file into this directory
−
date
 
−
cd $PBS_O_WORKDIR
 
−
../../../../zzz.programs/dock6_new/bin/dock6 -i denovo.in -o denovo.out
 
−
echo "Job finished on"
 
−
date                                                                     
 
  
 +
Create an input file
 +
touch rescore.in
  
−
===Denovo Rescore===
+
Complete the input file using the automated questions from dock
−
Create a directory for denovo rescore.  
+
dock6 -i rescore.in
−
mkdir denovo_rescore
 
−
Make sure you have ''1c87.final.denovo_build.mol2'' file in your directory and ''lig_withH_charge_1c87.mol2'' file will be your reference.
 
−
('''NOTE''': Tantamoto is a chemical similarity. 1.0 means identical to the reference. )
 
  
 
  conformer_search_type                                        rigid
 
  conformer_search_type                                        rigid
Line 150: Line 167:
 
  internal_energy_rep_exp                                      12
 
  internal_energy_rep_exp                                      12
 
  internal_energy_cutoff                                      100.0
 
  internal_energy_cutoff                                      100.0
−
  ligand_atom_file                                            1c87.final.denovo_build.mol2
+
  ligand_atom_file                                            output.denovo_build.mol2
 
  limit_max_ligands                                            no
 
  limit_max_ligands                                            no
 
  skip_molecule                                                no
 
  skip_molecule                                                no
−
  read_mol_solvation                                          no  
+
  read_mol_solvation                                          no
−
  calculate_rmsd                                              yes
+
  calculate_rmsd                                              no
−
use_rmsd_reference_mol                                      yes
 
−
rmsd_reference_filename                                      ../../001.files/lig_withH_charge_1c87.mol2
 
 
  use_database_filter                                          no
 
  use_database_filter                                          no
 
  orient_ligand                                                no
 
  orient_ligand                                                no
Line 180: Line 195:
 
  descriptor_use_multigrid_score                              no
 
  descriptor_use_multigrid_score                              no
 
  descriptor_use_continuous_score                              no
 
  descriptor_use_continuous_score                              no
−
  descriptor_use_footprint_similarity                          no
+
  descriptor_use_footprint_similarity                          yes
−
  descriptor_use_pharmacophore_score                          no
+
  descriptor_use_pharmacophore_score                          yes
 
  descriptor_use_tanimoto                                      yes
 
  descriptor_use_tanimoto                                      yes
 
  descriptor_use_hungarian                                    yes
 
  descriptor_use_hungarian                                    yes
−
  descriptor_use_volume_overlap                                no
+
  descriptor_use_volume_overlap                                yes
−
  descriptor_fingerprint_ref_filename                          ../../001.files/lig_withH_charge_1c87.mol2
+
descriptor_fps_score_use_footprint_reference_mol2            yes
−
  descriptor_hms_score_ref_filename                           ../../001.files/lig_withH_charge_1c87.mol2
+
descriptor_fps_score_footprint_reference_mol2_filename      candidate_mol_gen_frag.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                      ../../dock/2BXF.rec.withH.charged.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                      candidate_mol_gen_frag.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                          candidate_mol_gen_frag.mol2
 +
descriptor_hms_score_ref_filename                            candidate_mol_gen_frag.mol2
 
  descriptor_hms_score_matching_coeff                          -5
 
  descriptor_hms_score_matching_coeff                          -5
 
  descriptor_hms_score_rmsd_coeff                              1
 
  descriptor_hms_score_rmsd_coeff                              1
 +
descriptor_volume_score_reference_mol2_filename              candidate_mol_gen_frag.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_fingerprint_tanimoto                      -1
 
  descriptor_weight_hms_score                                  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                                                ../../dock/box/vdw_AMBER_parm99.defn
 +
flex_defn_file                                              ../../dock/dock/flex.defn
 +
flex_drive_file                                              ../../dock/dock/flex_drive.tbl
 +
chem_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/chem.defn
 +
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6/parameters/ph4.defn
 +
ligand_outfile_prefix                                        descriptor.output
 +
write_footprints                                            yes
 +
write_hbonds                                                yes
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 +
You will now have a file in your directory called descriptor.output_scored.mol2 which can be loaded into Chimera using ViewDock with your original ligand .mol2 file.
 +
 +
=='''II.''de-novo'' growth with PDB 2BXF (Generic)'''==
 +
In this section, the de novo growth will be done using a fragment library generated by many random ligands. This allows DOCK to generate novel ligands which are not restricted by the fragments and torsion environment of the crystal ligand.
 +
 +
In the previous section, single grid was used as the scoring function to generate the ligands. In this section, the interactions of the ligand with the most significant residues will be considered for the scoring function. In order to do so, multigrid scoring method where each of the significant residues will be described using unique grids, and a common grid for the rest of the residues.
 +
 +
===Specifying Primary Residues===
 +
First, the significant residues for the binding of the ligand has to be specified. Create unique directory for the generic de novo growth. Create an input file. (rescore.in) Use the following lines to generate the input file.
 +
 +
conformer_search_type                                        rigid
 +
use_internal_energy                                          no
 +
ligand_atom_file                                            ../2BXF_lig_withH.mol2 (use the ligand mol2 file)
 +
limit_max_ligands                                            no
 +
skip_molecule                                                no
 +
read_mol_solvation                                          no
 +
calculate_rmsd                                              no
 +
use_database_filter                                          no
 +
orient_ligand                                                no
 +
bump_filter                                                  no
 +
score_molecules                                              yes
 +
contact_score_primary                                        no
 +
contact_score_secondary                                      no
 +
grid_score_primary                                          no
 +
grid_score_secondary                                        no
 +
multigrid_score_primary                                      no
 +
multigrid_score_secondary                                    no
 +
dock3.5_score_primary                                        no
 +
dock3.5_score_secondary                                      no
 +
continuous_score_primary                                    no
 +
continuous_score_secondary                                  no
 +
footprint_similarity_score_primary                          yes
 +
footprint_similarity_score_secondary                        no
 +
fps_score_use_footprint_reference_mol2                      yes
 +
fps_score_footprint_reference_mol2_filename                  ../2BXF_lig_withH.mol2 (use the ligand mol2 file)
 +
fps_score_foot_compare_type                                  Euclidean
 +
fps_score_normalize_foot                                    no
 +
fps_score_foot_comp_all_residue                              no
 +
fps_score_choose_foot_range_type                            threshold
 +
fps_score_vdw_threshold                                      1
 +
fps_score_es_threshold                                      0.5
 +
fps_score_hb_threshold                                      0.5
 +
fps_score_use_remainder                                      yes
 +
fps_score_receptor_filename                                  ../2BXF_rec.mol2 (use the mol2 file for the receptor)
 +
fps_score_vdw_att_exp                                        6
 +
fps_score_vdw_rep_exp                                        12
 +
fps_score_vdw_rep_rad_scale                                  1
 +
fps_score_use_distance_dependent_dielectric                  yes
 +
fps_score_dielectric                                        4.0
 +
fps_score_vdw_fp_scale                                      1
 +
fps_score_es_fp_scale                                        1
 +
fps_score_hb_fp_scale                                        0
 +
pharmacophore_score_secondary                                no
 +
descriptor_score_secondary                                  no
 
  gbsa_zou_score_secondary                                    no
 
  gbsa_zou_score_secondary                                    no
 
  gbsa_hawkins_score_secondary                                no
 
  gbsa_hawkins_score_secondary                                no
Line 200: Line 318:
 
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
−
  ligand_outfile_prefix                                        devono_rescore.out  
+
  ligand_outfile_prefix                                        rescore.out
 +
write_footprints                                            yes
 +
write_hbonds                                                no
 
  write_orientations                                          no
 
  write_orientations                                          no
 
  num_scored_conformers                                        1
 
  num_scored_conformers                                        1
 
  rank_ligands                                                no
 
  rank_ligands                                                no
−
 
−
''devono_rescore.out_scored.mol2'' will be created.
 
−
Open Chimera and load ''lig_withH_charge_1c87.mol2'' file and viewdock to open ''devono_rescore.out_scored.mol2''
 
  
−
  [[File:Denovo rescore.png|thumb|center|1000px| Denovo Rescore]]
+
  dock6 -i rescore.in -o 2BXF.footprint_rescore.out
 +
 
 +
This will generate three output files.
 +
2BXF.footprint_rescore.out
 +
rescore.out_footprint_scored.txt
 +
rescore.out_scored.mol2
 +
 
 +
Use these files to specify the primary residues. Create a new file specify.sh using the following lines which are taken from previous tutorials and altered accordingly.
 +
 
 +
#!/bin/bash
 +
  grep -A 1 "range_union" 2BXF.footprint_rescore.out  |
 +
  grep -v "range_union" |
 +
  grep -v "\-" |
 +
  sed -e '{s/,/\n/g}' |
 +
  sed -e '{s/ //g}' |
 +
  sed '/^$/d' |
 +
  sort -n |
 +
  uniq > temp.dat
 +
  for i in `cat temp.dat`; do printf "%0*d\n" 3 $i; done > 2BXF.primary_residues.dat
 +
  for RES in `cat temp.dat`
 +
  do
 +
          grep " ${RES} " rescore.out_footprint_scored.txt  |
 +
          awk -v temp=${RES} '{if ($2 == temp) print $0;}' |
 +
          awk '{print $1 "  " $3 "  " $4}' >> reference.txt
 +
  done
 +
  grep "remainder" rescore.out_footprint_scored.txt |
 +
  sed -e '{s/,/  /g}' |
 +
  tr -d '\n' |
 +
  awk '{print $2 "  " $3 "  " $6}' >> reference.txt
 +
  mv reference.txt 2BXF.reference.txt
 +
  rm temp.dat
 +
 
 +
Use either of the following commands to specify the primary residues using the above file.
 +
chmod 770 specify.sh
 +
./specify.sh
 +
or
 +
bash specify.sh
 +
 
 +
This will generate another two files which specify the primary residues of the binding site of your receptor.
 +
2BXF.primary_residues.dat
 +
2BXF.reference.txt
 +
If it is successful, 13 residues should be specified as primary residues. (this is just for this system and the number of primary residues can change from system to system)
 +
 
 +
In the next section, grids will be generated for the primary residues and a common grid for the rest of the residues.
 +
 
 +
===Generation of grids===
 +
Create a new directory (multigrid)
 +
This will be done by a script file and two input files. The structure of each file is given below.
 +
 
 +
First input file (2BXF.multigrid.in)
 +
 
 +
compute_grids                  yes
 +
grid_spacing                  0.4
 +
output_molecule                yes
 +
contact_score                  no
 +
chemical_score                no
 +
energy_score                  yes
 +
energy_cutoff_distance        9999
 +
atom_model                    a
 +
attractive_exponent            6
 +
repulsive_exponent            9
 +
distance_dielectric            yes
 +
dielectric_factor              4
 +
bump_filter                    yes
 +
bump_overlap                  0.75
 +
receptor_file                  temp.mol2
 +
box_file                      ../../../dock/3.boxgrid/2BXF.box.pdb (use the virtual box generated in dock previously)
 +
vdw_definition_file            /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
 +
chemical_definition_file      /gpfs/projects/AMS536/zzz.programs/dock6/parameters/chem.defn
 +
score_grid_prefix              temp.rec
 +
receptor_out_file              temp.rec.grid.mol2
 +
 
 +
Second input file (2BXF.reference_multigridmin.in)
 +
 
 +
conformer_search_type                                        rigid
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
internal_energy_cutoff                                      100.0
 +
ligand_atom_file                                            ../../2BXF_lig_withH.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                                      yes
 +
multigrid_score_secondary                                    no
 +
multigrid_score_rep_rad_scale                                1.0
 +
multigrid_score_vdw_scale                                    1.0
 +
multigrid_score_es_scale                                    1.0
 +
multigrid_score_number_of_grids                              14                  (Should be the total number of primary residues + 1)
 +
multigrid_score_grid_prefix0                                2BXF.resid_380
 +
multigrid_score_grid_prefix1                                2BXF.resid_383
 +
multigrid_score_grid_prefix2                                2BXF.resid_384
 +
multigrid_score_grid_prefix3                                2BXF.resid_387
 +
multigrid_score_grid_prefix4                                2BXF.resid_399
 +
multigrid_score_grid_prefix5                                2BXF.resid_403
 +
multigrid_score_grid_prefix6                                2BXF.resid_407
 +
multigrid_score_grid_prefix7                                2BXF.resid_426
 +
multigrid_score_grid_prefix8                                2BXF.resid_429
 +
multigrid_score_grid_prefix9                                2BXF.resid_445
 +
multigrid_score_grid_prefix10                                2BXF.resid_446
 +
multigrid_score_grid_prefix11                                2BXF.resid_449
 +
multigrid_score_grid_prefix12                                2BXF.resid_481
 +
multigrid_score_grid_prefix13                                2BXF.resid_remaining  (rest of the residues)
 +
multigrid_score_fp_ref_mol                                  no
 +
multigrid_score_fp_ref_text                                  yes
 +
multigrid_score_footprint_text                              ../2BXF.reference.txt (generated earlier when specifying the primary residues)
 +
multigrid_score_foot_compare_type                            Euclidean
 +
multigrid_score_normalize_foot                              no
 +
multigrid_score_vdw_euc_scale                                1.0
 +
multigrid_score_es_euc_scale                                1.0
 +
dock3.5_score_secondary                                      no
 +
continuous_score_secondary                                  no
 +
footprint_similarity_score_secondary                        no
 +
pharmacophore_score_secondary                                no
 +
descriptor_score_secondary                                  no
 +
gbsa_zou_score_secondary                                    no
 +
gbsa_hawkins_score_secondary                                no
 +
SASA_score_secondary                                        no
 +
amber_score_secondary                                        no
 +
minimize_ligand                                              yes
 +
simplex_max_iterations                                      1000
 +
simplex_tors_premin_iterations                              0
 +
simplex_max_cycles                                          1
 +
simplex_score_converge                                      0.1
 +
simplex_cycle_converge                                      1.0
 +
simplex_trans_step                                          1.0
 +
simplex_rot_step                                            0.1
 +
simplex_tors_step                                            10.0
 +
simplex_random_seed                                          0
 +
simplex_restraint_min                                        no
 +
atom_model                                                  all
 +
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
 +
flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
 +
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 +
ligand_outfile_prefix                                        output
 +
write_footprints                                            no
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
 
 +
Use the following script to generate the grids. (multigrid.sh)
  
−
==De novo design with PDB 1C87 generic fragment library==
+
export PRIMARY_RES=` cat ../2BXF.primary_residues.dat | sed -e 's/\n/ /g' `
−
===Assembling your fragment library===
+
export DOCKHOME="/gpfs/projects/AMS536/zzz.programs/dock6"
 +
python ${DOCKHOME}/bin/multigrid_fp_gen.py ../../2BXF_rec.mol2 2BXF.resid 2BXF.multigrid.in ${PRIMARY_RES}
 +
rm temp.mol2
 +
rm 2BXF.resid_*.rec.grid.mol2
 +
${DOCKHOME}/bin/dock6 -i 2BXF.reference_multigridmin.in -o 2BXF.reference_multigridmin.out
 +
mv output_scored.mol2 2BXF.lig.multigridmin.mol2
 +
cp 2BXF.lig.multigridmin.mol2 ../multi-grid
  
−
Actually, you won't be assembling anything. For this method we are using a generic set of fragments which we will use to grow our ligands. Like with the focused library, the traits of the cognate ligand will guide our designing algorithm so that we do not get anything too far-fetched.
+
Run the above script to generate the grids
 +
bash multigrid.sh
  
−
Make a new directory for these calculations
+
If it is successful, grids will be generated. Check 2BXF.lig.multigridmin.out file to make sure everything is okay.
  
−
mkdir denovo_growth_generic
+
===Running de novo growth ===
 +
In this section, a de novo growth will be done using the grids generated above and a provided fragment library where the fragments are generated from random drug like ligandsprovided in the dock6 distribution in the parameters directory.
  
−
Now we will need an input file like before, but we will take a closer look at some of the parameters. In particular, we want to make sure we are using an appropriate amount of starting fragments (not too many or it will be a combinatorial explosion).
+
Go one directory back from multigrid and create a new directory, denovo. Copy the neccesary fragment library files needed into this directory. (scaffold,linker,sidechain,torsion env ..etc) Then create an input file for denovo growth using the lines below and save as denovo.in.
  
 
  conformer_search_type                                        denovo
 
  conformer_search_type                                        denovo
−
  dn_fraglib_scaffold_file                                    /PATH/fraglib_scaffold.mol2
+
  dn_fraglib_scaffold_file                                    fraglib_scaffold.mol2
−
  dn_fraglib_linker_file                                      /PATH/fraglib_linker.mol2
+
  dn_fraglib_linker_file                                      fraglib_linker.mol2
−
  dn_fraglib_sidechain_file                                    /PATH/fraglib_sidechain.mol2
+
  dn_fraglib_sidechain_file                                    fraglib_sidechain.mol2
 
  dn_user_specified_anchor                                    no
 
  dn_user_specified_anchor                                    no
 
  dn_use_torenv_table                                          yes
 
  dn_use_torenv_table                                          yes
−
  dn_torenv_table                                              /PATH/fraglib_torenv.dat
+
  dn_torenv_table                                              fraglib_torenv.dat
 
  dn_sampling_method                                          graph
 
  dn_sampling_method                                          graph
 
  dn_graph_max_picks                                          30
 
  dn_graph_max_picks                                          30
Line 236: Line 509:
 
  dn_pruning_conformer_score_scaling_factor                    1.0
 
  dn_pruning_conformer_score_scaling_factor                    1.0
 
  dn_pruning_clustering_cutoff                                100.0
 
  dn_pruning_clustering_cutoff                                100.0
−
  dn_constraint_mol_wt                                        300
+
  dn_constraint_mol_wt                                        550.0
 
  dn_constraint_rot_bon                                        15
 
  dn_constraint_rot_bon                                        15
 
  dn_constraint_formal_charge                                  2.0
 
  dn_constraint_formal_charge                                  2.0
Line 242: Line 515:
 
  dn_heur_matched_rmsd                                        2.0
 
  dn_heur_matched_rmsd                                        2.0
 
  dn_unique_anchors                                            1
 
  dn_unique_anchors                                            1
−
  dn_max_grow_layers                                          4
+
  dn_max_grow_layers                                          9
 
  dn_max_root_size                                            25
 
  dn_max_root_size                                            25
 
  dn_max_layer_size                                            25
 
  dn_max_layer_size                                            25
 
  dn_max_current_aps                                          5
 
  dn_max_current_aps                                          5
−
  dn_max_scaffolds_per_layer                                  2
+
  dn_max_scaffolds_per_layer                                  1
 
  dn_write_checkpoints                                        yes
 
  dn_write_checkpoints                                        yes
 
  dn_write_prune_dump                                          no
 
  dn_write_prune_dump                                          no
 
  dn_write_orients                                            no
 
  dn_write_orients                                            no
 
  dn_write_growth_trees                                        no
 
  dn_write_growth_trees                                        no
−
  dn_output_prefix                                            out
+
  dn_output_prefix                                            output
 
  use_internal_energy                                          yes
 
  use_internal_energy                                          yes
 
  internal_energy_rep_exp                                      12
 
  internal_energy_rep_exp                                      12
Line 258: Line 531:
 
  orient_ligand                                                yes
 
  orient_ligand                                                yes
 
  automated_matching                                          yes
 
  automated_matching                                          yes
−
  receptor_site_file                                          ../surface-spheres/selected_spheres.sph
+
  receptor_site_file                                          ../2.surface_spheres/selected_spheres.sph
 
  max_orientations                                            1000
 
  max_orientations                                            1000
 
  critical_points                                              no
 
  critical_points                                              no
Line 290: Line 563:
 
  descriptor_multigrid_score_vdw_scale                        1.0
 
  descriptor_multigrid_score_vdw_scale                        1.0
 
  descriptor_multigrid_score_es_scale                          1.0
 
  descriptor_multigrid_score_es_scale                          1.0
−
  descriptor_multigrid_score_number_of_grids                  26
+
  descriptor_multigrid_score_number_of_grids                  14
−
  descriptor_multigrid_score_grid_prefix0                      ../multi-grid/1c87.resid_023
+
  descriptor_multigrid_score_grid_prefix0                      ../15.multi-grid/2BXF.resid_380
−
  descriptor_multigrid_score_grid_prefix1                      ../multi-grid/1c87.resid_035
+
  descriptor_multigrid_score_grid_prefix1                      ../15.multi-grid/2BXF.resid_383
−
  descriptor_multigrid_score_grid_prefix2                      ../multi-grid/1c87.resid_044
+
  descriptor_multigrid_score_grid_prefix2                      ../15.multi-grid/2BXF.resid_384
−
  descriptor_multigrid_score_grid_prefix3                      ../multi-grid/1c87.resid_045
+
  descriptor_multigrid_score_grid_prefix3                      ../15.multi-grid/2BXF.resid_387
−
  descriptor_multigrid_score_grid_prefix4                      ../multi-grid/1c87.resid_046
+
  descriptor_multigrid_score_grid_prefix4                      ../15.multi-grid/2BXF.resid_399
−
  descriptor_multigrid_score_grid_prefix5                      ../multi-grid/1c87.resid_047
+
  descriptor_multigrid_score_grid_prefix5                      ../15.multi-grid/2BXF.resid_403
−
  descriptor_multigrid_score_grid_prefix6                      ../multi-grid/1c87.resid_048
+
  descriptor_multigrid_score_grid_prefix6                      ../15.multi-grid/2BXF.resid_407
−
  descriptor_multigrid_score_grid_prefix7                      ../multi-grid/1c87.resid_111
+
  descriptor_multigrid_score_grid_prefix7                      ../15.multi-grid/2BXF.resid_426
−
  descriptor_multigrid_score_grid_prefix8                      ../multi-grid/1c87.resid_114
+
  descriptor_multigrid_score_grid_prefix8                      ../15.multi-grid/2BXF.resid_429
−
  descriptor_multigrid_score_grid_prefix9                      ../multi-grid/1c87.resid_115
+
  descriptor_multigrid_score_grid_prefix9                      ../15.multi-grid/2BXF.resid_445
−
  descriptor_multigrid_score_grid_prefix10                    ../multi-grid/1c87.resid_119
+
  descriptor_multigrid_score_grid_prefix10                    ../15.multi-grid/2BXF.resid_446
−
  descriptor_multigrid_score_grid_prefix11                    ../multi-grid/1c87.resid_180
+
  descriptor_multigrid_score_grid_prefix11                    ../15.multi-grid/2BXF.resid_449
−
  descriptor_multigrid_score_grid_prefix12                    ../multi-grid/1c87.resid_181
+
  descriptor_multigrid_score_grid_prefix12                    ../15.multi-grid/2BXF.resid_481
−
  descriptor_multigrid_score_grid_prefix13                    ../multi-grid/1c87.resid_185
+
  descriptor_multigrid_score_grid_prefix13                    ../15.multi-grid/2BXF.resid_remaining
−
descriptor_multigrid_score_grid_prefix14                    ../multi-grid/1c87.resid_214
+
  descriptor_multigrid_score_fp_ref_mol                        yes
−
descriptor_multigrid_score_grid_prefix15                    ../multi-grid/1c87.resid_215
+
  descriptor_multigrid_score_footprint_ref                    ../4.dock/2BXF.lig.min_scored.mol2
−
descriptor_multigrid_score_grid_prefix16                    ../multi-grid/1c87.resid_216
 
−
descriptor_multigrid_score_grid_prefix17                    ../multi-grid/1c87.resid_217
 
−
descriptor_multigrid_score_grid_prefix18                    ../multi-grid/1c87.resid_218
 
−
descriptor_multigrid_score_grid_prefix19                    ../multi-grid/1c87.resid_219
 
−
descriptor_multigrid_score_grid_prefix20                    ../multi-grid/1c87.resid_220
 
−
descriptor_multigrid_score_grid_prefix21                    ../multi-grid/1c87.resid_253
 
−
descriptor_multigrid_score_grid_prefix22                    ../multi-grid/1c87.resid_256
 
−
descriptor_multigrid_score_grid_prefix23                    ../multi-grid/1c87.resid_261
 
−
descriptor_multigrid_score_grid_prefix24                    ../multi-grid/1c87.resid_264
 
−
descriptor_multigrid_score_grid_prefix25                    ../multi-grid/1c87.resid_remaining
 
−
  descriptor_multigrid_score_fp_ref_mol                        no
 
−
descriptor_multigrid_score_fp_ref_text                      yes
 
−
  descriptor_multigrid_score_footprint_text                    ../multi-grid/1c87.reference.txt
 
 
  descriptor_multigrid_score_foot_compare_type                Euclidean
 
  descriptor_multigrid_score_foot_compare_type                Euclidean
 
  descriptor_multigrid_score_normalize_foot                    no
 
  descriptor_multigrid_score_normalize_foot                    no
Line 345: Line 605:
 
  simplex_restraint_min                                        no
 
  simplex_restraint_min                                        no
 
  atom_model                                                  all
 
  atom_model                                                  all
−
  vdw_defn_file                                                ../files/vdw_AMBER_parm99.defn
+
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
−
  flex_defn_file                                              ../files/flex.defn
+
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
−
  flex_drive_file                                              ../files/flex_drive.tbl
+
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
 +
 
 +
Use the following script (denovo.sh) to submit the job to the cluster.
 +
#!/bin/bash
 +
#PBS -l walltime=48:00:00
 +
#PBS -l nodes=1:ppn=28
 +
#PBS -q long
 +
#PBS -N 2BXF_denovo
 +
#PBS -V
 +
cd $PBS_O_WORKDIR
 +
dock6 -i denovo.in -o 2BXF_denovo.out
 +
 +
Use the following command to submit the job.
 +
qsub denovo.sh

Latest revision as of 12:58, 10 March 2020

I. de-novo design with PDB 2BXF (Focused)

Fragment Libraries

A focused fragment library will be used in this tutorial, in order to attempt building the same ligand. A focused fragment library can be generated using the same ligand.

Create a new directory for the fragment library. 

mkdir fraglib

Inside the fraglib directory create a new input file for fragment generation. 

touch fraglib.in

Generate the fragments by calling the input file through DOCK6 

dock6 -i fraglib.in

Answer the prompted questions interactively using the following lines. 

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                                             /Path_to_file/2BXF_lig_withH.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                                           /Path_to_file/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/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        output
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Once fragment generation is completed, following files will be generated. (fraglib_linker.mol2, fraglib_rigid.mol2, fraglib_scaffold.mol2, fraglib_sidechain.mol2, fraglib_torenv.dat) Open the mol2 files using chimera and check if the fragments match with the ligand used for fragment generation.

2BXF sidechain fragment

Focused Denovo Growth

The generated fragments will be used to perform the de novo dock. Here the fragments will added together restricted by different properties like maximum layers, formal charge and molecular weight. Before each connection, DOCK will check with the torsion environment file created in frgment generation to see if that particular connection is seen before. If not the connection won't be made.

Create a new directory for denovo dock. 

mkdir denovo

Create a new input file for denovo dock. 

touch denovo.in

Run the input file through dock. 

dock6 -i denovo.in

Answer the prompted question interactively using the following lines.

conformer_search_type denovo 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     /8.fraglib/fraglib_scaffold.mol2
dn_fraglib_linker_file                                       /8.fraglib/fraglib_linker.mol2
dn_fraglib_sidechain_file                                    /8.fraglib/fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              /8.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                                             2BXF.final
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                                           /2.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                                       /3.boxgrid/grid
multigrid_score_secondary                                    no
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              yes
minimize_anchor                                              yes
minimize_flexible_growth                                     yes
use_advanced_simplex_parameters                              no
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_anchor_max_iterations                                500
simplex_grow_max_iterations                                  500
simplex_grow_tors_premin_iterations                          0
simplex_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
2BXF growthed molecules

Focused Denovo Rescore

Create a new directory 

mkdir focuseddenovorescore

Copy your reference .mol2 file into this directory

Create an input file 

touch rescore.in

Complete the input file using the automated questions from dock 

dock6 -i rescore.in

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             output.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       candidate_mol_gen_frag.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                       ../../dock/2BXF.rec.withH.charged.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                       candidate_mol_gen_frag.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                          candidate_mol_gen_frag.mol2
descriptor_hms_score_ref_filename                            candidate_mol_gen_frag.mol2
descriptor_hms_score_matching_coeff                          -5
descriptor_hms_score_rmsd_coeff                              1
descriptor_volume_score_reference_mol2_filename              candidate_mol_gen_frag.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                                                ../../dock/box/vdw_AMBER_parm99.defn
flex_defn_file                                               ../../dock/dock/flex.defn
flex_drive_file                                              ../../dock/dock/flex_drive.tbl
chem_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/chem.defn
pharmacophore_defn_file                                      /gpfs/projects/AMS536/zzz.programs/dock6/parameters/ph4.defn
ligand_outfile_prefix                                        descriptor.output
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

You will now have a file in your directory called descriptor.output_scored.mol2 which can be loaded into Chimera using ViewDock with your original ligand .mol2 file.

II.de-novo growth with PDB 2BXF (Generic)

In this section, the de novo growth will be done using a fragment library generated by many random ligands. This allows DOCK to generate novel ligands which are not restricted by the fragments and torsion environment of the crystal ligand.

In the previous section, single grid was used as the scoring function to generate the ligands. In this section, the interactions of the ligand with the most significant residues will be considered for the scoring function. In order to do so, multigrid scoring method where each of the significant residues will be described using unique grids, and a common grid for the rest of the residues.

Specifying Primary Residues

First, the significant residues for the binding of the ligand has to be specified. Create unique directory for the generic de novo growth. Create an input file. (rescore.in) Use the following lines to generate the input file. 

conformer_search_type                                        rigid
use_internal_energy                                          no
ligand_atom_file                                             ../2BXF_lig_withH.mol2 (use the ligand mol2 file)
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          no
orient_ligand                                                no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
multigrid_score_primary                                      no
multigrid_score_secondary                                    no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
footprint_similarity_score_primary                           yes
footprint_similarity_score_secondary                         no
fps_score_use_footprint_reference_mol2                       yes
fps_score_footprint_reference_mol2_filename                  ../2BXF_lig_withH.mol2 (use the ligand mol2 file)
fps_score_foot_compare_type                                  Euclidean
fps_score_normalize_foot                                     no
fps_score_foot_comp_all_residue                              no
fps_score_choose_foot_range_type                             threshold
fps_score_vdw_threshold                                      1
fps_score_es_threshold                                       0.5
fps_score_hb_threshold                                       0.5
fps_score_use_remainder                                      yes
fps_score_receptor_filename                                  ../2BXF_rec.mol2 (use the mol2 file for the receptor)
fps_score_vdw_att_exp                                        6
fps_score_vdw_rep_exp                                        12
fps_score_vdw_rep_rad_scale                                  1
fps_score_use_distance_dependent_dielectric                  yes
fps_score_dielectric                                         4.0
fps_score_vdw_fp_scale                                       1
fps_score_es_fp_scale                                        1
fps_score_hb_fp_scale                                        0
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        rescore.out
write_footprints                                             yes
write_hbonds                                                 no
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

dock6 -i rescore.in -o 2BXF.footprint_rescore.out

This will generate three output files. 

2BXF.footprint_rescore.out 
rescore.out_footprint_scored.txt
rescore.out_scored.mol2

Use these files to specify the primary residues. Create a new file specify.sh using the following lines which are taken from previous tutorials and altered accordingly. 

#!/bin/bash
  grep -A 1 "range_union" 2BXF.footprint_rescore.out  |
  grep -v "range_union" |
  grep -v "\-" |
  sed -e '{s/,/\n/g}' |
  sed -e '{s/ //g}' |
  sed '/^$/d' |
  sort -n |
  uniq > temp.dat
  for i in `cat temp.dat`; do printf "%0*d\n" 3 $i; done > 2BXF.primary_residues.dat
  for RES in `cat temp.dat`
  do
          grep " ${RES} " rescore.out_footprint_scored.txt  |
          awk -v temp=${RES} '{if ($2 == temp) print $0;}' |
          awk '{print $1 "  " $3 "  " $4}' >> reference.txt
  done
  grep "remainder" rescore.out_footprint_scored.txt |
  sed -e '{s/,/  /g}' |
  tr -d '\n' |
  awk '{print $2 "  " $3 "  " $6}' >> reference.txt
  mv reference.txt 2BXF.reference.txt
  rm temp.dat

Use either of the following commands to specify the primary residues using the above file. 

chmod 770 specify.sh
./specify.sh

or 

bash specify.sh

This will generate another two files which specify the primary residues of the binding site of your receptor. 

2BXF.primary_residues.dat
2BXF.reference.txt

If it is successful, 13 residues should be specified as primary residues. (this is just for this system and the number of primary residues can change from system to system)

In the next section, grids will be generated for the primary residues and a common grid for the rest of the residues.

Generation of grids

Create a new directory (multigrid) This will be done by a script file and two input files. The structure of each file is given below.

First input file (2BXF.multigrid.in) 

compute_grids                  yes
grid_spacing                   0.4
output_molecule                yes
contact_score                  no
chemical_score                 no
energy_score                   yes
energy_cutoff_distance         9999
atom_model                     a
attractive_exponent            6
repulsive_exponent             9
distance_dielectric            yes
dielectric_factor              4
bump_filter                    yes
bump_overlap                   0.75
receptor_file                  temp.mol2
box_file                       ../../../dock/3.boxgrid/2BXF.box.pdb (use the virtual box generated in dock previously)
vdw_definition_file            /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
chemical_definition_file       /gpfs/projects/AMS536/zzz.programs/dock6/parameters/chem.defn
score_grid_prefix              temp.rec
receptor_out_file              temp.rec.grid.mol2

Second input file (2BXF.reference_multigridmin.in) 

conformer_search_type                                        rigid
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
internal_energy_cutoff                                       100.0
ligand_atom_file                                             ../../2BXF_lig_withH.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                                      yes
multigrid_score_secondary                                    no
multigrid_score_rep_rad_scale                                1.0
multigrid_score_vdw_scale                                    1.0
multigrid_score_es_scale                                     1.0
multigrid_score_number_of_grids                              14                  (Should be the total number of primary residues + 1)
multigrid_score_grid_prefix0                                 2BXF.resid_380
multigrid_score_grid_prefix1                                 2BXF.resid_383
multigrid_score_grid_prefix2                                 2BXF.resid_384
multigrid_score_grid_prefix3                                 2BXF.resid_387
multigrid_score_grid_prefix4                                 2BXF.resid_399
multigrid_score_grid_prefix5                                 2BXF.resid_403
multigrid_score_grid_prefix6                                 2BXF.resid_407
multigrid_score_grid_prefix7                                 2BXF.resid_426
multigrid_score_grid_prefix8                                 2BXF.resid_429
multigrid_score_grid_prefix9                                 2BXF.resid_445
multigrid_score_grid_prefix10                                2BXF.resid_446
multigrid_score_grid_prefix11                                2BXF.resid_449
multigrid_score_grid_prefix12                                2BXF.resid_481
multigrid_score_grid_prefix13                                2BXF.resid_remaining  (rest of the residues)
multigrid_score_fp_ref_mol                                   no
multigrid_score_fp_ref_text                                  yes
multigrid_score_footprint_text                               ../2BXF.reference.txt (generated earlier when specifying the primary residues)
multigrid_score_foot_compare_type                            Euclidean
multigrid_score_normalize_foot                               no
multigrid_score_vdw_euc_scale                                1.0
multigrid_score_es_euc_scale                                 1.0
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
footprint_similarity_score_secondary                         no
pharmacophore_score_secondary                                no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
SASA_score_secondary                                         no
amber_score_secondary                                        no
minimize_ligand                                              yes
simplex_max_iterations                                       1000
simplex_tors_premin_iterations                               0
simplex_max_cycles                                           1
simplex_score_converge                                       0.1
simplex_cycle_converge                                       1.0
simplex_trans_step                                           1.0
simplex_rot_step                                             0.1
simplex_tors_step                                            10.0
simplex_random_seed                                          0
simplex_restraint_min                                        no
atom_model                                                   all
vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl
ligand_outfile_prefix                                        output
write_footprints                                             no
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no

Use the following script to generate the grids. (multigrid.sh) 

export PRIMARY_RES=` cat ../2BXF.primary_residues.dat | sed -e 's/\n/ /g' `
export DOCKHOME="/gpfs/projects/AMS536/zzz.programs/dock6"
python ${DOCKHOME}/bin/multigrid_fp_gen.py ../../2BXF_rec.mol2 2BXF.resid 2BXF.multigrid.in ${PRIMARY_RES}
rm temp.mol2
rm 2BXF.resid_*.rec.grid.mol2
${DOCKHOME}/bin/dock6 -i 2BXF.reference_multigridmin.in -o 2BXF.reference_multigridmin.out
mv output_scored.mol2 2BXF.lig.multigridmin.mol2
cp 2BXF.lig.multigridmin.mol2 ../multi-grid

Run the above script to generate the grids 

bash multigrid.sh

If it is successful, grids will be generated. Check 2BXF.lig.multigridmin.out file to make sure everything is okay.

Running de novo growth

In this section, a de novo growth will be done using the grids generated above and a provided fragment library where the fragments are generated from random drug like ligandsprovided in the dock6 distribution in the parameters directory.

Go one directory back from multigrid and create a new directory, denovo. Copy the neccesary fragment library files needed into this directory. (scaffold,linker,sidechain,torsion env ..etc) Then create an input file for denovo growth using the lines below and save as denovo.in. 

conformer_search_type                                        denovo
dn_fraglib_scaffold_file                                     fraglib_scaffold.mol2
dn_fraglib_linker_file                                       fraglib_linker.mol2
dn_fraglib_sidechain_file                                    fraglib_sidechain.mol2
dn_user_specified_anchor                                     no
dn_use_torenv_table                                          yes
dn_torenv_table                                              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                                             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                                           ../2.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                                    no
descriptor_use_multigrid_score                               yes
descriptor_use_pharmacophore_score                           no
descriptor_use_tanimoto                                      no
descriptor_use_hungarian                                     no
descriptor_use_volume_overlap                                no
descriptor_multigrid_score_rep_rad_scale                     1.0
descriptor_multigrid_score_vdw_scale                         1.0
descriptor_multigrid_score_es_scale                          1.0
descriptor_multigrid_score_number_of_grids                   14
descriptor_multigrid_score_grid_prefix0                      ../15.multi-grid/2BXF.resid_380
descriptor_multigrid_score_grid_prefix1                      ../15.multi-grid/2BXF.resid_383
descriptor_multigrid_score_grid_prefix2                      ../15.multi-grid/2BXF.resid_384
descriptor_multigrid_score_grid_prefix3                      ../15.multi-grid/2BXF.resid_387
descriptor_multigrid_score_grid_prefix4                      ../15.multi-grid/2BXF.resid_399
descriptor_multigrid_score_grid_prefix5                      ../15.multi-grid/2BXF.resid_403
descriptor_multigrid_score_grid_prefix6                      ../15.multi-grid/2BXF.resid_407
descriptor_multigrid_score_grid_prefix7                      ../15.multi-grid/2BXF.resid_426
descriptor_multigrid_score_grid_prefix8                      ../15.multi-grid/2BXF.resid_429
descriptor_multigrid_score_grid_prefix9                      ../15.multi-grid/2BXF.resid_445
descriptor_multigrid_score_grid_prefix10                     ../15.multi-grid/2BXF.resid_446
descriptor_multigrid_score_grid_prefix11                     ../15.multi-grid/2BXF.resid_449
descriptor_multigrid_score_grid_prefix12                     ../15.multi-grid/2BXF.resid_481
descriptor_multigrid_score_grid_prefix13                     ../15.multi-grid/2BXF.resid_remaining
descriptor_multigrid_score_fp_ref_mol                        yes
descriptor_multigrid_score_footprint_ref                     ../4.dock/2BXF.lig.min_scored.mol2
descriptor_multigrid_score_foot_compare_type                 Euclidean
descriptor_multigrid_score_normalize_foot                    no
descriptor_multigrid_score_vdw_euc_scale                     1.0
descriptor_multigrid_score_es_euc_scale                      1.0
descriptor_weight_multigrid_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/parameters/vdw_AMBER_parm99.defn
flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex.defn
flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6/parameters/flex_drive.tbl

Use the following script (denovo.sh) to submit the job to the cluster. 

#!/bin/bash
#PBS -l walltime=48:00:00
#PBS -l nodes=1:ppn=28
#PBS -q long
#PBS -N 2BXF_denovo
#PBS -V
cd $PBS_O_WORKDIR
dock6 -i denovo.in -o 2BXF_denovo.out

Use the following command to submit the job. 

qsub denovo.sh
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