Difference between revisions of "2022 Denovo tutorial 3 with PDBID 1X70"

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==System Preparation==
+
=Focused Denovo Design=
−
'''Directory Setup'''
 
  
−
ATTENTION: This tutorial requires you to have first completed the 2022 1X70 VS tutorial: https://ringo.ams.stonybrook.edu/index.php/2022_DOCK_tutorial_3_with_PDBID_1X70
+
In this tutorial, we will be making a focus fragment library from the crystallographic ligand for PDB 1X70 and then attempting to rebuild the cognate ligand with the library we generated.
 +
 
 +
===Ligand Fragmentation===
 +
 
 +
'''ATTENTION:'''
 +
This tutorial requires you to have first completed the 2022 1X70 VS tutorial: https://ringo.ams.stonybrook.edu/index.php/2022_DOCK_tutorial_3_with_PDBID_1X70
  
 
Make a new directory:  
 
Make a new directory:  
Line 8: Line 12:
 
   mkdir 09.focus_dn
 
   mkdir 09.focus_dn
  
−
Now inside 09.focus_dn, make the following DOCK6 input file:
+
Now inside 09.focus_dn, make the following DOCK6 input file: "fraglib.in"
  
 +
  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                                            ../01.structures/715.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                                          ../02.spheres/selected_spheres.sph
 +
  max_orientations                                            1000
 +
  critical_points                                              no
 +
  chemical_matching                                            no
 +
  use_ligand_spheres                                          no
 +
  bump_filter                                                  no
 +
  score_molecules                                              no
 +
  atom_model                                                  all
 +
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
 +
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
 +
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 +
  ligand_outfile_prefix                                        fragment.out
 +
  write_orientations                                          no
 +
  num_scored_conformers                                        1
 +
  rank_ligands                                                no
  
 +
  dock6 -i fraglib.in -o fraglib.out
 +
 +
You should end up with 5 different files:
 +
 +
  "fraglib_rigid.mol2  fraglib_scaffold.mol2  fraglib_sidechain.mol2  fraglib_torenv.dat fraglib_linker.mol2"
 +
 +
Each file contains fragments defined by the number of places they were cut at during fragment generation.
  
 
Now load up Chimera:
 
Now load up Chimera:
  
−
   Tools > Binding/Surface Analysis > View Dock > Load each of the fragment libraries
+
   Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2
  
  
Line 20: Line 63:
 
[[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]]
 
[[File:1X70_linkers.png|thumb|center|800px|All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715]]
  
 +
  Load fraglib_sidechain.mol2
 +
 +
[[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from fraglib_sidechain.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715]]
 +
 +
  Load both
 +
 +
[[File:715_frags.png|thumb|center|800px|All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top) ]]
 +
 +
===Focused Growth===
 +
 +
Make the following dock6 input file: "focus.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                                            4
 +
  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                                            yes
 +
  dn_write_growth_trees                                        yes
 +
  dn_output_prefix                                            dn_focus.out
 +
  use_internal_energy                                          yes
 +
  internal_energy_rep_exp                                      12
 +
  internal_energy_cutoff                                      100.0
 +
  use_database_filter                                          no
 +
  orient_ligand                                                yes
 +
  automated_matching                                          yes
 +
  receptor_site_file                                          ../02.spheres/selected_spheres.sph
 +
  max_orientations                                            1000
 +
  critical_points                                              no
 +
  chemical_matching                                            no
 +
  use_ligand_spheres                                          no
 +
  bump_filter                                                  no
 +
  score_molecules                                              yes
 +
  contact_score_primary                                        no
 +
  contact_score_secondary                                      no
 +
  grid_score_primary                                          yes
 +
  grid_score_secondary                                        no
 +
  grid_score_rep_rad_scale                                    1
 +
  grid_score_vdw_scale                                        1
 +
  grid_score_es_scale                                          1
 +
  grid_score_grid_prefix                                      ../03.grid/grid
 +
  multigrid_score_secondary                                    no
 +
  dock3.5_score_secondary                                      no
 +
  continuous_score_secondary                                  no
 +
  footprint_similarity_score_secondary                        no
 +
  pharmacophore_score_secondary                                no
 +
  descriptor_score_secondary                                  no
 +
  gbsa_zou_score_secondary                                    no
 +
  gbsa_hawkins_score_secondary                                no
 +
  SASA_score_secondary                                        no
 +
  amber_score_secondary                                        no
 +
  minimize_ligand                                              yes
 +
  minimize_anchor                                              yes
 +
  minimize_flexible_growth                                    yes
 +
  use_advanced_simplex_parameters                              no
 +
  simplex_max_cycles                                          1
 +
  simplex_score_converge                                      0.1
 +
  simplex_cycle_converge                                      1.0
 +
  simplex_trans_step                                          1.0
 +
  simplex_rot_step                                            0.1
 +
  simplex_tors_step                                            10.0
 +
  simplex_anchor_max_iterations                                500
 +
  simplex_grow_max_iterations                                  500
 +
  simplex_grow_tors_premin_iterations                          0
 +
  simplex_random_seed                                          0
 +
  simplex_restraint_min                                        no
 +
  atom_model                                                  all
 +
  vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_de_novo.defn
 +
  flex_defn_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
 +
  flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 +
 +
  dock6 -i focus.in -o focus.out
 +
 +
You should get the following file: "dn_focus.out.denovo_build.mol2"
 +
 +
Load in the denovo results Chimera using viewdock, then load in the refence ligand:
 +
 +
  Tools > general controls > model panel > set the reference ligand to inactive and then move the fragments so they are not overlayed
 +
 +
[[File:1X70_focus_dn.png|thumb|center|800px|The first dozen focus denovo results and the view dock interface]]
 +
 +
[[File:1X70_focus_dn_pose.png|thumb|center|800px|The top scoring pose from the focus denovo (top) and the original pose of crystallographic ligand (bottom)]]
  
−
[[File:1X70_sidechains.png|thumb|center|800px|All of the sidechains from fraglib_linker.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715]]
+
As we can see, the top scoring poses consist of the original crystallographic ligand in various posses.

Latest revision as of 10:39, 21 March 2022

Focused Denovo Design

In this tutorial, we will be making a focus fragment library from the crystallographic ligand for PDB 1X70 and then attempting to rebuild the cognate ligand with the library we generated.

Ligand Fragmentation

ATTENTION: This tutorial requires you to have first completed the 2022 1X70 VS tutorial: https://ringo.ams.stonybrook.edu/index.php/2022_DOCK_tutorial_3_with_PDBID_1X70

Make a new directory: 

 mkdir 09.focus_dn

Now inside 09.focus_dn, make the following DOCK6 input file: "fraglib.in" 

 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                                             ../01.structures/715.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                                           ../02.spheres/selected_spheres.sph
 max_orientations                                             1000
 critical_points                                              no
 chemical_matching                                            no
 use_ligand_spheres                                           no
 bump_filter                                                  no
 score_molecules                                              no
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 ligand_outfile_prefix                                        fragment.out
 write_orientations                                           no
 num_scored_conformers                                        1
 rank_ligands                                                 no

 dock6 -i fraglib.in -o fraglib.out

You should end up with 5 different files: 

 "fraglib_rigid.mol2  fraglib_scaffold.mol2  fraglib_sidechain.mol2  fraglib_torenv.dat fraglib_linker.mol2"

Each file contains fragments defined by the number of places they were cut at during fragment generation.

Now load up Chimera: 

 Tools > Binding/Surface Analysis > View Dock > Load fraglib_linker.mol2


All of the linkers from fraglib_linker.mol2, fragments with 2 non-Hydrogen rotatable bonds in 715
 Load fraglib_sidechain.mol2
All of the sidechains from fraglib_sidechain.mol2, fragments with 1 non-Hydrogen rotatable bonds in 715
 Load both
All of the fragments from 715 loaded in (bottom, sea blue) and 715.mol2 (top)

Focused Growth

Make the following dock6 input file: "focus.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                                            4
 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                                             yes
 dn_write_growth_trees                                        yes
 dn_output_prefix                                             dn_focus.out
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 use_database_filter                                          no
 orient_ligand                                                yes
 automated_matching                                           yes
 receptor_site_file                                           ../02.spheres/selected_spheres.sph
 max_orientations                                             1000
 critical_points                                              no
 chemical_matching                                            no
 use_ligand_spheres                                           no
 bump_filter                                                  no
 score_molecules                                              yes
 contact_score_primary                                        no
 contact_score_secondary                                      no
 grid_score_primary                                           yes
 grid_score_secondary                                         no
 grid_score_rep_rad_scale                                     1
 grid_score_vdw_scale                                         1
 grid_score_es_scale                                          1
 grid_score_grid_prefix                                       ../03.grid/grid
 multigrid_score_secondary                                    no
 dock3.5_score_secondary                                      no
 continuous_score_secondary                                   no
 footprint_similarity_score_secondary                         no
 pharmacophore_score_secondary                                no
 descriptor_score_secondary                                   no
 gbsa_zou_score_secondary                                     no
 gbsa_hawkins_score_secondary                                 no
 SASA_score_secondary                                         no
 amber_score_secondary                                        no
 minimize_ligand                                              yes
 minimize_anchor                                              yes
 minimize_flexible_growth                                     yes
 use_advanced_simplex_parameters                              no
 simplex_max_cycles                                           1
 simplex_score_converge                                       0.1
 simplex_cycle_converge                                       1.0
 simplex_trans_step                                           1.0
 simplex_rot_step                                             0.1
 simplex_tors_step                                            10.0
 simplex_anchor_max_iterations                                500
 simplex_grow_max_iterations                                  500
 simplex_grow_tors_premin_iterations                          0
 simplex_random_seed                                          0
 simplex_restraint_min                                        no
 atom_model                                                   all
 vdw_defn_file                                                /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/vdw_de_novo.defn
 flex_defn_file                                               /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/AMS536/zzz.programs/dock6.9_release/parameters/flex_drive.tbl

 dock6 -i focus.in -o focus.out

You should get the following file: "dn_focus.out.denovo_build.mol2"

Load in the denovo results Chimera using viewdock, then load in the refence ligand: 

 Tools > general controls > model panel > set the reference ligand to inactive and then move the fragments so they are not overlayed
The first dozen focus denovo results and the view dock interface
The top scoring pose from the focus denovo (top) and the original pose of crystallographic ligand (bottom)

As we can see, the top scoring poses consist of the original crystallographic ligand in various posses.

Retrieved from "https://ringo.ams.stonybrook.edu/index.php?title=2022_Denovo_tutorial_3_with_PDBID_1X70&oldid=14980"