View source for Ligand Enrichment Tutorial

The purpose of this tutorial is to develop a uniform method to test ligand enrichment across the Rizzo lab with the DOCK software. 

==I.Introduction==
Ligand Enrichment is a common experiment used to evaluate how well a docking program is capable of accurately modeling in vitro experiments. This experiment uses active ligands and decoy ligands to access a docking programs ability to successfully dock to a target site. These active and decoy ligands are roughly the same size and differ due to chemical similarities. These active ligands should bind more favorably(Have a lower energy score) then the decoy ligands if the docking program can accurately model these binding site and ligand interactions. 


The 3 major outcomes for this experiment are early enrichment, random enrichment, and late enrichment. Early enrichment indicates the active ligands dock more successful in the experiment(The goal for all docking programs). The second is random enrichment indicating that the docking program can differentiate between active and decoy. Late enrichment indicating that docking software gives the lowest energy scores to the decoys which is the worst outcome. The other factor to consider is the degree of early and late enrichment

==II.Prepping systems==
-The first step is to create a directory for the system you are preparing

     mkdir 1Q4X

-The first step is to obtain the active and decoy ligand test set systems which can be found on the Schoichet DUD-E test set website http://dude.docking.org/targets

-Once these targets are obtained unzip these files using the gzip command to get the active and decoy forms 
 gzip -d actives_final.mol2.gz 
 gzip -d decoys_final.mol2.gz 
    
-Prepare the target receptor by either using the official test set ligands or manually prepare a receptor target from scratch

Following all these steps your directory should look like the following using the 1QRX system 

     actives_final.mol2
     decoys_final.mol2
     1Q4X.rec.clean.mol2

==III.Docking molecules==
-After completing this step a virtual screen will be conducted using mpi for both the active and decoy ligands seperately

-The input parameters are as follows for the active ligands

 conformer_search_type                                        flex
 write_fragment_libraries                                     no
 user_specified_anchor                                        no
 limit_max_anchors                                            no
 min_anchor_size                                              5
 pruning_use_clustering                                       yes
 pruning_max_orients                                          1000
 pruning_clustering_cutoff                                    100
 pruning_conformer_score_cutoff                               100.0
 pruning_conformer_score_scaling_factor                       1.0
 use_clash_overlap                                            no
 write_growth_tree                                            no
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 ligand_atom_file                                             actives_final.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                                           /gpfs/projects/rizzo/ccorbo/2020_DUDE_0.3_gridspacing/DUDE_Good_to_go/1Q4X/1Q4X.rec.clust.close.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                                       /gpfs/projects/rizzo/ccorbo/2020_DUDE_0.3_gridspacing/DUDE_Good_to_go/1Q4X/1Q4X.rec
 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/rizzo/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 ligand_outfile_prefix                                        1Q4X.active.output.mpi
 write_orientations                                           no
 num_scored_conformers                                        1
 rank_ligands                                                 no

-The input parameters for the decoy ligands.

 conformer_search_type                                        flex
 write_fragment_libraries                                     no
 user_specified_anchor                                        no
 limit_max_anchors                                            no
 min_anchor_size                                              5
 pruning_use_clustering                                       yes
 pruning_max_orients                                          1000
 pruning_clustering_cutoff                                    100
 pruning_conformer_score_cutoff                               100.0
 pruning_conformer_score_scaling_factor                       1.0
 use_clash_overlap                                            no
 write_growth_tree                                            no
 use_internal_energy                                          yes
 internal_energy_rep_exp                                      12
 internal_energy_cutoff                                       100.0
 ligand_atom_file                                             decoys_final.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                                           /gpfs/projects/rizzo/ccorbo/2020_DUDE_0.3_gridspacing/DUDE_Good_to_go/1Q4X/1Q4X.rec.clust.close.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                                       /gpfs/projects/rizzo/ccorbo/2020_DUDE_0.3_gridspacing/DUDE_Good_to_go/1Q4X/1Q4X.rec
 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/rizzo/zzz.programs/dock6.9_release/parameters/vdw_AMBER_parm99.defn
 flex_defn_file                                               /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex.defn
 flex_drive_file                                              /gpfs/projects/rizzo/zzz.programs/dock6.9_release/parameters/flex_drive.tbl
 ligand_outfile_prefix                                        1Q4X.decoy.output.mpi
 write_orientations                                           no
 num_scored_conformers                                        1
 rank_ligands                                                 no


-Then submit the script to the qsub to dock the molecule in parallel. Some of the ligand active and decoy testsets are quite large so mpi submission is recommended.
 #!/bin/bash
 #SBATCH --partition=rn-long-40core
 #SBATCH --time=48:00:00
 #SBATCH --nodes=4
 #SBATCH --ntasks=160
 #SBATCH --job-name=1B9V_mpi_runs
 #SBATCH --output=1B9V_mpi_runs

 cd $SLURM_SUBMIT_DIR
 module load intel/mpi/64/2018/18.0.3
 mpirun -np 160 dock6.mpi -i 1Q4X_active_mpi.in -o 1Q4X_decoy_mpi.out
 mpirun -np 160 dock6.mpi -i 1Q4X_decoy_mpi.in -o 1Q4X_decoy_mpi.out

==IV.Ligand Enrichment Analysis==

-Lastly, 2 scripts were developed to analyze the results. One script to generate a CSV file and a secondary script that uses the CSV data to create a graph.

-The script that generates the CSV file takes three parameters, the list of systems, name of decoy ligands mol2 file, name of active ligands mol2 file.
(NOTE: This script can generate multiple CSV files for different ligand experiments, but the naming of the active and decoy mol2 files must be the same)
Example:
python roc_curve_lig_enrichment_v2.py 1Q4X.txt decoys_final.mol2 actives_final.mol2