Virtual Screening Protocol on BlueGene (IGF-IR system)
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)
