View source for 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)