Difference between revisions of "Virtual Screening Protocol on BlueGene (IGF-IR system)"

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For this document, virtual screening protocol will be described in detail for IGF-IR system (by Yulin Huang).  
 
For this document, virtual screening protocol will be described in detail for IGF-IR system (by Yulin Huang).  
  
−
'''1.''' '''Identify the target'''  
+
'''1.''' '''Identify the Target'''  
  
 
This is the very fist step for virtual screening.  Usually, a single or multiple proteins are selected as targets if their mutations or overexpression are implicated in certain diseases.  However, disease relevance alone is not sufficient for target identification.  Moreover, the target must be druggable which means the target should be predicted to bind to a drug with high affinity and this binding will bring therapeutic benefit to the patients.  The target is defined as druggable if there are drugs already identified for it.  Otherwise, druggability can be predicted using evolution rules, structural properties or other destructors.     
 
This is the very fist step for virtual screening.  Usually, a single or multiple proteins are selected as targets if their mutations or overexpression are implicated in certain diseases.  However, disease relevance alone is not sufficient for target identification.  Moreover, the target must be druggable which means the target should be predicted to bind to a drug with high affinity and this binding will bring therapeutic benefit to the patients.  The target is defined as druggable if there are drugs already identified for it.  Otherwise, druggability can be predicted using evolution rules, structural properties or other destructors.     
  
−
'''2.''' '''Prepare the target'''  
+
'''2.''' '''Prepare the Target'''  
  
−
At this step, you need to prepare the protein structure used for virtual screening.  The structures can be downloaded from PDB database if they are available.  Make sure which form of the structures Or the structures can be obtained from homology modeling or molecular dynamic simulations.  Monoatomic ions should be carefully treated and usually they are treated as part of the receptor if they were within ca. 10Å from the binding site.  In terms of water molecules, prior knowledge is needed for decisions.  If the system is known to have water-mediated interactions (i.e, ErbB family receptors), then the waters should be included as part of the receptors.  If not, waters should be removed.  For histidine residues, they are treated based  on the environment, i.e., which nitrogen was coordinated with ions and/or ligands.  Finally, all the protein structures are aligned to a common frame (added hydrogen and minimize the H).
+
At this step, you need to prepare the protein structure used for virtual screening.  The structures can be downloaded from PDB database if they are available.  Make sure which form of the structure should be used. For example, for IGF-IR system, PDB structures have been released for active, inactive, and intermediate forms.  Or the structures can be obtained from homology modeling or molecular dynamic simulations.  All the protein structures are aligned to a common frame and processed with AMBER tleap program. Hydrogen was added and minimized and force field parameters were assigned. Monoatomic ions should be carefully treated and usually they are treated as part of the receptor if they were within ca. 10Å from the binding site.  In terms of water molecules, prior knowledge is needed for decisions.  If the system is known to have water-mediated interactions (i.e, ErbB family receptors), then the waters should be included as part of the receptors.  If not, waters should be removed.  For histidine residues, they are treated based  on the environment, i.e., which nitrogen was coordinated with ions and/or ligands.   
  
 
'''3.''' '''Database Preparation'''  
 
'''3.''' '''Database Preparation'''  
  
 +
Database was prepared by William T. Berger and Trent Balius.  The database used was Chemdiv with 969572 molecules.  Chemdiv was reranked based on number of rotatable bonds.  Firstly, a mol2 file was generated with molecules of  rotatable bond 0 to rotatable bond 7. Each chunk (No1 to NO10) evenly store 6000 molecules with rotatable bonds less than 7.  Chunk11 was for molecules with rotatable bonds equal to 7.  Chunk 12 to Chunk 20 each evenly store 3000 molecules with rotatable bonds of 8 to 15 and chunk 21 store the left molecules.  Therefore, the reranked database was split into 21 chunks and virtual screening can be finished within the time limit of the supercomputer BlueGene.
  
 
'''4.'''        '''Run Docking on Bluegene'''
 
'''4.'''        '''Run Docking on Bluegene'''
  
 
(1) Make the grid for the protein.
 
(1) Make the grid for the protein.
 +
 +
For IGF-IR system, active (PDB 2ZM3), inactive (PDB 3NW5) and intermediate forms(PDB 3D94)are used.  For this document, only results for 3D94 are reported.
  
 
cat <<EOF >box.in
 
cat <<EOF >box.in
Line 23: Line 26:
 
  box.pdb
 
  box.pdb
 
  EOF
 
  EOF
−
 
  
 
cat <<EOF >grid.in
 
cat <<EOF >grid.in
Line 47: Line 49:
 
  receptor_out_file                                            ./${system}.rec.grid.mol2
 
  receptor_out_file                                            ./${system}.rec.grid.mol2
 
EOF
 
EOF
−
 
−
 
  
 
Among them, the parameters are set as follows:  
 
Among them, the parameters are set as follows:  
Line 56: Line 56:
 
set box_margin = 8
 
set box_margin = 8
  
 +
(2) Dock to the Database
 +
 +
The compound database in this study is ChemDiv.  The database was split into 21 chunks. Docking was running on BlueGene 512 block and clock was set to 48 hours.  For this step, the basic flexible docking protocol was used.  Note that in order to eliminate the ligands with bad descriptors, database filter was set for heavy atoms,rotatable bonds, molecular weight, formal charge and xlogp.
  
−
(2) Dock to the subset of the database
 
 
  ligand_atom_file                                            ${ligfile}
 
  ligand_atom_file                                            ${ligfile}
 
  limit_max_ligands                                            no
 
  limit_max_ligands                                            no
Line 126: Line 128:
 
  flex_defn_file                                              $defn_dir/flex.defn
 
  flex_defn_file                                              $defn_dir/flex.defn
 
  flex_drive_file                                              $defn_dir/flex_drive.tbl
 
  flex_drive_file                                              $defn_dir/flex_drive.tbl
−
  ligand_outfile_prefix                                                                         ${system}.${vendor}.${chunk}.100.flx.${protocol}.dock2grid
+
  ligand_outfile_prefix                                                                           ${system}.${vendor}.${chunk}.100.flx.${protocol}.dock2grid
 
  write_orientations                                          no
 
  write_orientations                                          no
 
  num_scored_conformers                                        1
 
  num_scored_conformers                                        1
Line 132: Line 134:
 
  rank_ligands                                                no
 
  rank_ligands                                                no
 
  EOFA
 
  EOFA
 +
 +
(3) Minimize off the Grid
 +
 +
This step is also running on BlueGene 512 block.
 +
 +
cat << EOFB > ${system}.$vendor.${chunk}.200.flx.${protocol}.min.in
 +
ligand_atom_file                                            ${system}.${vendor}.${chunk}.100.flx.${protocol}.dock2grid_scored.mol2
 +
limit_max_ligands                                            no
 +
skip_molecule                                                no
 +
read_mol_solvation                                          no
 +
calculate_rmsd                                              no
 +
orient_ligand                                                no
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
flexible_ligand                                              no
 +
bump_filter                                                  no
 +
score_molecules                                              yes
 +
contact_score_primary                                        no
 +
contact_score_secondary                                      no
 +
grid_score_primary                                          no
 +
grid_score_secondary                                        no
 +
dock3.5_score_primary                                        no
 +
dock3.5_score_secondary                                      no
 +
continuous_score_primary                                    yes
 +
continuous_score_secondary                                  no
 +
cont_score_rec_filename                                      ${recfile}
 +
cont_score_att_exp                                          6
 +
cont_score_rep_exp                                          12
 +
cont_score_rep_rad_scale                                    1
 +
cont_score_use_dist_dep_dielectric                          yes
 +
cont_score_dielectric                                        4.0
 +
cont_score_vdw_scale                                        1
 +
cont_score_es_scale                                          1
 +
descriptor_score_secondary                                  no
 +
gbsa_zou_score_secondary                                    no
 +
gbsa_hawkins_score_secondary                                no
 +
amber_score_secondary                                        no
 +
minimize_ligand                                              yes
 +
simplex_max_iterations                                      500
 +
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
 +
restraint_min                                                yes
 +
coefficient_restraint                                        10.0
 +
atom_model                                                  all
 +
vdw_defn_file                                                $defn_dir/vdw_AMBER_parm99.defn
 +
flex_defn_file                                              $defn_dir/flex.defn
 +
flex_drive_file                                              $defn_dir/flex_drive.tbl
 +
ligand_outfile_prefix                                        ${system}.$vendor.${chunk}.200.flx.${protocol}.min
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
EOFB
 +
 +
(4) Footprint Rescoring
 +
 +
This step is running on BlueGene 32 block. The poses are rescored by footprint.
 +
 +
cat << EOFA > ${system}.${vendor}.${chunk}.300.flx.${protocol}.footprint.in
 +
ligand_atom_file                                            ${minoffgrid_file}
 +
limit_max_ligands                                            no
 +
skip_molecule                                                no
 +
read_mol_solvation                                          no
 +
calculate_rmsd                                              no
 +
orient_ligand                                                no
 +
use_internal_energy                                          yes
 +
internal_energy_rep_exp                                      12
 +
flexible_ligand                                              no
 +
bump_filter                                                  no
 +
score_molecules                                              yes
 +
contact_score_primary                                        no
 +
contact_score_secondary                                      no
 +
grid_score_primary                                          no
 +
grid_score_secondary                                        no
 +
dock3.5_score_primary                                        no
 +
dock3.5_score_secondary                                      no
 +
continuous_score_primary                                    no
 +
continuous_score_secondary                                  no
 +
descriptor_score_primary                                    yes
 +
descriptor_score_secondary                                  no
 +
use_footprint_reference_mol2                                yes
 +
footprint_reference_mol2_filename                            ${fp_ref}
 +
desc_foot_compare_type                                      d
 +
desc_normalize_foot                                          yes
 +
desc_foot_comp_all_residue                                  yes
 +
desc_score_rec_filename                                      ${recfile}
 +
desc_score_att_exp                                          6
 +
desc_score_rep_exp                                          12
 +
desc_score_rep_rad_scale                                    1
 +
use_distance_dependent_dielectric                            yes
 +
desc_score_dielectric                                        4.0
 +
desc_score_vdw_scale                                        1
 +
desc_score_es_scale                                          1
 +
desc_score_hb_scale                                          0
 +
desc_score_internal_scale                                    0
 +
desc_score_fp_vwd_scale                                      0
 +
desc_score_fp_es_scale                                      0
 +
desc_score_fp_hb_scale                                      0
 +
gbsa_zou_score_secondary                                    no
 +
gbsa_hawkins_score_secondary                                no
 +
amber_score_secondary                                        no
 +
minimize_ligand                                              no
 +
atom_model                                                  all
 +
vdw_defn_file                                                $defn_dir/vdw_AMBER_parm99.defn
 +
flex_defn_file                                              $defn_dir/flex.defn
 +
flex_drive_file                                              $defn_dir/flex_drive.tbl
 +
ligand_outfile_prefix                                          ${system}.$vendor.${chunk}.300.flx.${protocol}.footprint
 +
write_footprints                                            yes
 +
write_hbonds                                                yes
 +
write_orientations                                          no
 +
num_scored_conformers                                        1
 +
rank_ligands                                                no
 +
EOFA
 +
 +
(5) Sort and Obtain the Top Poses
 +
There are 7 sorting criteria. 
 +
A. HBond
 +
B. VDW footprint
 +
C. Electrostatic footprint
 +
D. HBond footprint
 +
E. The footprint sum of (VDW + ES)
 +
F. The footprint sum of (VDW + ES + HBond)
 +
G. score of (VDW + ES + internal energy)

Latest revision as of 15:06, 25 July 2012

For this document, virtual screening protocol will be described in detail for IGF-IR system (by Yulin Huang).

1. Identify the Target

This is the very fist step for virtual screening. Usually, a single or multiple proteins are selected as targets if their mutations or overexpression are implicated in certain diseases. However, disease relevance alone is not sufficient for target identification. Moreover, the target must be druggable which means the target should be predicted to bind to a drug with high affinity and this binding will bring therapeutic benefit to the patients. The target is defined as druggable if there are drugs already identified for it. Otherwise, druggability can be predicted using evolution rules, structural properties or other destructors.

2. Prepare the Target

At this step, you need to prepare the protein structure used for virtual screening. The structures can be downloaded from PDB database if they are available. Make sure which form of the structure should be used. For example, for IGF-IR system, PDB structures have been released for active, inactive, and intermediate forms. Or the structures can be obtained from homology modeling or molecular dynamic simulations. All the protein structures are aligned to a common frame and processed with AMBER tleap program. Hydrogen was added and minimized and force field parameters were assigned. Monoatomic ions should be carefully treated and usually they are treated as part of the receptor if they were within ca. 10Å from the binding site. In terms of water molecules, prior knowledge is needed for decisions. If the system is known to have water-mediated interactions (i.e, ErbB family receptors), then the waters should be included as part of the receptors. If not, waters should be removed. For histidine residues, they are treated based on the environment, i.e., which nitrogen was coordinated with ions and/or ligands.

3. Database Preparation

Database was prepared by William T. Berger and Trent Balius. The database used was Chemdiv with 969572 molecules. Chemdiv was reranked based on number of rotatable bonds. Firstly, a mol2 file was generated with molecules of rotatable bond 0 to rotatable bond 7. Each chunk (No1 to NO10) evenly store 6000 molecules with rotatable bonds less than 7. Chunk11 was for molecules with rotatable bonds equal to 7. Chunk 12 to Chunk 20 each evenly store 3000 molecules with rotatable bonds of 8 to 15 and chunk 21 store the left molecules. Therefore, the reranked database was split into 21 chunks and virtual screening can be finished within the time limit of the supercomputer BlueGene.

4. Run Docking on Bluegene

(1) Make the grid for the protein.

For IGF-IR system, active (PDB 2ZM3), inactive (PDB 3NW5) and intermediate forms(PDB 3D94)are used. For this document, only results for 3D94 are reported.

cat <<EOF >box.in 

yes
$box_margin
./selected_spheres.sph
1
box.pdb
EOF

cat <<EOF >grid.in 

compute_grids                                                yes
grid_spacing                                                 $grid_spacing
output_molecule                                              yes
contact_score                                                no
chemical_score                                               no
energy_score                                                 yes
energy_cutoff_distance                                       999
atom_model                                                   a
attractive_exponent                                          ${attractive}
repulsive_exponent                                           ${repulsive}
distance_dielectric                                          yes
dielectric_factor                                            4
bump_filter                                                  yes
bump_overlap                                                 0.75
receptor_file                                                ./receptor.mol2
box_file                                                     ./box.pdb
vdw_definition_file                                          ./vdw.defn
chemical_definition_file                                     ./chem.defn
score_grid_prefix                                            ./${system}.rec
receptor_out_file                                            ./${system}.rec.grid.mol2

EOF

Among them, the parameters are set as follows: set grid_spacing = 0.3 set attractive = 6 set repulsive = 9 set box_margin = 8

(2) Dock to the Database

The compound database in this study is ChemDiv. The database was split into 21 chunks. Docking was running on BlueGene 512 block and clock was set to 48 hours. For this step, the basic flexible docking protocol was used. Note that in order to eliminate the ligands with bad descriptors, database filter was set for heavy atoms,rotatable bonds, molecular weight, formal charge and xlogp. 

ligand_atom_file                                             ${ligfile}
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
use_database_filter                                          yes
dbfilter_max_heavy_atoms                                     1000
dbfilter_min_heavy_atoms                                     0
dbfilter_max_rot_bonds                                       15
dbfilter_min_rot_bonds                                       0
dbfilter_max_molwt                                           10000
dbfilter_min_molwt                                           0
dbfilter_max_formal_charge                                   2
dbfilter_min_formal_charge                                   -2
dbfilter_max_xlogp                                           20
dbfilter_min_xlogp                                           -20
orient_ligand                                                yes
automated_matching                                           yes
receptor_site_file                                           ${sphfile}
max_orientations                                             1000
critical_points                                              no
chemical_matching                                            no
use_ligand_spheres                                           no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
flexible_ligand                                              yes
min_anchor_size                                              5
pruning_use_clustering                                       yes
pruning_max_orients                                          1000
pruning_clustering_cutoff                                    100
pruning_conformer_score_cutoff                               100
use_clash_overlap                                            no
print_growth_tree                                            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                                       ${gridprefix}
dock3.5_score_secondary                                      no
continuous_score_secondary                                   no
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_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
restraint_min                                                no
atom_model                                                   all
vdw_defn_file                                                $defn_dir/vdw_AMBER_parm99.defn
flex_defn_file                                               $defn_dir/flex.defn
flex_drive_file                                              $defn_dir/flex_drive.tbl
ligand_outfile_prefix                                                                           ${system}.${vendor}.${chunk}.100.flx.${protocol}.dock2grid
write_orientations                                           no
num_scored_conformers                                        1
write_conformations                                          no
rank_ligands                                                 no
EOFA

(3) Minimize off the Grid

This step is also running on BlueGene 512 block.

cat << EOFB > ${system}.$vendor.${chunk}.200.flx.${protocol}.min.in 

ligand_atom_file                                            ${system}.${vendor}.${chunk}.100.flx.${protocol}.dock2grid_scored.mol2
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     yes
continuous_score_secondary                                   no
cont_score_rec_filename                                      ${recfile}
cont_score_att_exp                                           6
cont_score_rep_exp                                           12
cont_score_rep_rad_scale                                     1
cont_score_use_dist_dep_dielectric                           yes
cont_score_dielectric                                        4.0
cont_score_vdw_scale                                         1
cont_score_es_scale                                          1
descriptor_score_secondary                                   no
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
amber_score_secondary                                        no
minimize_ligand                                              yes
simplex_max_iterations                                       500
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
restraint_min                                                yes
coefficient_restraint                                        10.0
atom_model                                                   all
vdw_defn_file                                                $defn_dir/vdw_AMBER_parm99.defn
flex_defn_file                                               $defn_dir/flex.defn
flex_drive_file                                              $defn_dir/flex_drive.tbl
ligand_outfile_prefix                                         ${system}.$vendor.${chunk}.200.flx.${protocol}.min
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no
EOFB

(4) Footprint Rescoring

This step is running on BlueGene 32 block. The poses are rescored by footprint.

cat << EOFA > ${system}.${vendor}.${chunk}.300.flx.${protocol}.footprint.in 

ligand_atom_file                                             ${minoffgrid_file}
limit_max_ligands                                            no
skip_molecule                                                no
read_mol_solvation                                           no
calculate_rmsd                                               no
orient_ligand                                                no
use_internal_energy                                          yes
internal_energy_rep_exp                                      12
flexible_ligand                                              no
bump_filter                                                  no
score_molecules                                              yes
contact_score_primary                                        no
contact_score_secondary                                      no
grid_score_primary                                           no
grid_score_secondary                                         no
dock3.5_score_primary                                        no
dock3.5_score_secondary                                      no
continuous_score_primary                                     no
continuous_score_secondary                                   no
descriptor_score_primary                                     yes
descriptor_score_secondary                                   no
use_footprint_reference_mol2                                 yes
footprint_reference_mol2_filename                            ${fp_ref}
desc_foot_compare_type                                       d
desc_normalize_foot                                          yes
desc_foot_comp_all_residue                                   yes
desc_score_rec_filename                                      ${recfile}
desc_score_att_exp                                           6
desc_score_rep_exp                                           12
desc_score_rep_rad_scale                                     1
use_distance_dependent_dielectric                            yes
desc_score_dielectric                                        4.0
desc_score_vdw_scale                                         1
desc_score_es_scale                                          1
desc_score_hb_scale                                          0
desc_score_internal_scale                                    0
desc_score_fp_vwd_scale                                      0
desc_score_fp_es_scale                                       0
desc_score_fp_hb_scale                                       0
gbsa_zou_score_secondary                                     no
gbsa_hawkins_score_secondary                                 no
amber_score_secondary                                        no
minimize_ligand                                              no
atom_model                                                   all
vdw_defn_file                                                $defn_dir/vdw_AMBER_parm99.defn
flex_defn_file                                               $defn_dir/flex.defn
flex_drive_file                                              $defn_dir/flex_drive.tbl
ligand_outfile_prefix                                          ${system}.$vendor.${chunk}.300.flx.${protocol}.footprint
write_footprints                                             yes
write_hbonds                                                 yes
write_orientations                                           no
num_scored_conformers                                        1
rank_ligands                                                 no
EOFA

(5) Sort and Obtain the Top Poses
There are 7 sorting criteria.  
A. HBond
B. VDW footprint
C. Electrostatic footprint
D. HBond footprint
E. The footprint sum of (VDW + ES) 
F. The footprint sum of (VDW + ES + HBond) 
G. score of (VDW + ES + internal energy)
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