2017 Denovo design tutorial 2 with PDB 4QMZ
Contents
2017 Denovo design tutorial 2 with PDB 4QMZ
The Denovo module of DOCK is a relatively new feature as of Fall 2016 that constructs new ligand molecules inside a protein active site from a library of user-specified "fragments." These novel ligand molecules are scored based on a number of unique scoring algorithms/criteria specified. The fragments used are common chemical functional groups -- or building blocks -- that are typically selected from a ZINC library of millions of compounds based off of their frequency of appearance. These fragments are classified as scaffolds, linkers, or side chains, according to the number of atomic positions that are permitted to seed growth: 3, 2, and 1 atoms, respectively. Thus, a scaffold could seed growth from three different atoms, having three linkers bonded to each position, and a linker could seed growth on two positions, and a side-chain on one position. Once the molecules are built within the active site, their interactions with the protein are scored using the user-specified method of scoring. This tutorial will walk through the steps needed to run a Denovo calculation on the 4QMZ system from the 2017 DOCK tutorial. This method will utilize the multi-grid scoring function, called through the descriptor score. Ensure you have all the folders and files necessary from running the 2017 tutorial. Users are encouraged to run through the traditional DOCK tutorial for the 4qmz system as many of the files are recycled for the denovo experiments. Before running the calculation, it's worth looking through the "Things to Keep in Mind" section at the bottom for some good pieces of information.
Additional Files Needed
To run the Denovo code with multigrid scoring you need these files:
fraglib_scaffold.mol2 <-- LIRed
fraglib_linker.mol2 <-- LIRed
fraglib_sidechain.mol2 <-- LIRed
anchor_library.mol2 <--LIRed
fraglib_torenv.dat <-- LIRed
selected_spheres.sph <-- make your own
primary_residues_multigrid.bmp / .nrg <-- make your own
multigrid_minimized_ligand.mol2 <-- make your own
vdw_AMBER_parm99.defn <--needed for regular dock
flex.defn <--needed for regular dock
flex_drive.tbl <-- needed for regular dock
vdw_DumHyd.defn (needed for scoring functions other than multigrid) <-- LIRed
The fragment libraries and parameter files must be obtained prior to the Denovo calculation, and can be found on LIRed through the paths:
/gpfs/home/guest43/scratch/denovo/trial_denovo/000.fraglib
/trial_denovo/zzz.parameters/
Everything else is generated through this tutorial, prior to running the Denovo code.
Preparing The Files
Before running Denovo on 4QMZ, please ensure you have gone through the DOCK 2017 tutorial and have all the resulting files. The tutorial can be accessed through here. You should have these files in your directory:
4qmz.pdb
4qmz.lig.mol2
4qmz.rec.clean.mol2
4qmz.rec.noH.mol2
selected_spheres.sph
Additionally, you will also need these parameter files:
vdw_AMBER_parm99.defn
flex.defn
flex_drive.tbl
In order to run Denovo with multigrid scoring, we must first go through several steps:
1). Create a primary residue text file and a reference text file -- selects the primary residues of interest.
2). Make a multigrid file for each specified residue -- forms a grid for each residue specified in previous step.
3). Minimizes ligand mol2 file using multigrids from previous step.
4). Rescores ligand on multigrid to yield a minimized ligand .mol2 file. This serves as the reference ligand for Denovo calculations.
Luckily, our good friend Brian generated some extremely robust scripts to make this process easier. There is one script for each step, but we will only use the simple input files for DOCK. If you are interested in using the scripts (and a lot of debugging), they can be found on lired under: /gfps/home/guest43/scratch/denovo/trial_denovo/run/ .
Dock Specifying Primary Residues
Create a directory within your working directory titled 008.footprint_rescore. This is where all pertinent files from this step will go, and where we will run our calculation from. The input file for this step should be titled 4qmz.footprint_rescore.in, and should look like (substitute your own directory path ~/your/own/directory/01.dockprep/4qmz.lig.mol2) :
conformer_search_type rigid use_internal_energy no ligand_atom_file /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd no use_database_filter no orient_ligand no bump_filter no score_molecules yes contact_score_primary no contact_score_secondary no grid_score_primary no grid_score_secondary no multigrid_score_primary no multigrid_score_secondary no dock3.5_score_primary no dock3.5_score_secondary no continuous_score_primary no continuous_score_secondary no footprint_similarity_score_primary yes footprint_similarity_score_secondary no fps_score_use_footprint_reference_mol2 yes fps_score_footprint_reference_mol2_filename /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.lig.mol2 fps_score_foot_compare_type Euclidean fps_score_normalize_foot no fps_score_foot_comp_all_residue no fps_score_choose_foot_range_type threshold fps_score_vdw_threshold 1 fps_score_es_threshold 0.5 fps_score_hb_threshold 0.5 fps_score_use_remainder yes fps_score_receptor_filename /gpfs/home/stelehany/rizzo_rot_research/dock_tutorial/01.dockprep/4qmz.rec.mol2 fps_score_vdw_att_exp 6 fps_score_vdw_rep_exp 12 fps_score_vdw_rep_rad_scale 1 fps_score_use_distance_dependent_dielectric yes fps_score_dielectric 4.0 fps_score_vdw_fp_scale 1 fps_score_es_fp_scale 1 fps_score_hb_fp_scale 0 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 no atom_model all vdw_defn_file /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/vdw_AMBER_parm99.defn flex_defn_file /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex.defn flex_drive_file /gpfs/projects/AMS536/zzz.programs/dn_dock.6.7/parameters/flex_drive.tbl ligand_outfile_prefix output write_footprints yes write_hbonds no write_orientations no num_scored_conformers 1 rank_ligands no
This calculation should be very quick (~10 seconds) and result in three output files:
4qmz.footprint_rescore.out output_footprint_scored.txt output_scored.mol2
Now, we must declare the primary residues in the active site and generate a grid file for each. Create a new file in the text editor named 4qmz.primary_residues.sh and write this inside of it (copied from Brian's script *.fpsrescore.qsub.sh):
#!/bin/bash
grep -A 1 "range_union" footprintrescore.out |
grep -v "range_union" |
grep -v "\-" |
sed -e '{s/,/\n/g}' |
sed -e '{s/ //g}' |
sed '/^$/d' |
sort -n |
uniq > temp.dat
for i in `cat temp.dat`; do printf "%0*d\n" 3 $i; done > 4qmz.primary_residues.dat
for RES in `cat temp.dat`
do
grep " ${RES} " output_footprint_scored.txt |
awk -v temp=${RES} '{if ($2 == temp) print $0;}' |
awk '{print $1 " " $3 " " $4}' >> reference.txt
done
grep "remainder" output_footprint_scored.txt |
sed -e '{s/,/ /g}' |
tr -d '\n' |
awk '{print $2 " " $3 " " $6}' >> reference.txt
mv reference.txt 4qmz.reference.txt
rm temp.dat
Run the script and you should have two new files:
4qmz.primary_residues.dat 4qmz.reference.txt
These are our primary residues! Now we need to generate a grid for each one.
