Difference between revisions of "DOCK Denovo Run"

Revision as of 18:37, 16 November 2016

Dock Denovo Run

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 fragments 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 on 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 Beta Trypsin system from the 2016 DOCK tutorial. This method will utilize the multi-grid scoring function, called through the descriptor score.

Preparing The Files

Before the Denovo module can be run, please ensure you have ran the DOCK 2016 tutorial and have all the resulting files. The tutorial can be accessed through here.

You should have these files in your directory:

001.files:

    1BJU.pdb
    1BJU.lig.mol2
    1BJU.rec.clean.mol2
    1BJU.rec.noH.mol2
    selected_spheres.sph

Additionally, you will also need these parameter files:

zzz.parameters:

    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 1BJU.footpring_rescore.in, and should look like:

conformer_search_type rigid

    use_internal_energy                                          no
    ligand_atom_file                                             ${WORKDIR}/001.files/1BJU.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_use_footprint_reference_mol2                             yes
    fps_footprint_reference_mol2_filename                        ${WORKDIR}/001.files/1BJU.lig.mol2
    fps_foot_compare_type                                        d
    fps_normalize_foot                                           no
    fps_foot_comp_all_residue                                    no
    fps_choose_foot_range_type                                   threshold
    fps_vdw_threshold                                            1
    fps_es_threshold                                             0.5
    fps_hb_threshold                                             0.5
    fps_use_remainder                                            yes
    fps_receptor_filename                                        ${WORKDIR}/001.files/1BJU.rec.clean.mol2
    fps_vdw_att_exp                                              6
    fps_vdw_rep_exp                                              12
    fps_vdw_rep_rad_scale                                        1
    fps_use_distance_dependent_dielectric                        yes
    fps_dielectric                                               4.0
    fps_vdw_fp_scale                                             1
    fps_es_fp_scale                                              1
    fps_hb_fp_scale                                              0
    descriptor_score_secondary                                   no
    gbsa_zou_score_secondary                                     no
    gbsa_hawkins_score_secondary                                 no
    SASA_descriptor_score_secondary                              no
    amber_score_secondary                                        no
    minimize_ligand                                              no
    atom_model                                                   all
    vdw_defn_file                                                ${WORKDIR}/001.files/vdw_AMBER_parm99.defn
    flex_defn_file                                               ${WORKDIR}/001.files/flex.defn
    flex_drive_file                                              ${WORKDIR}/001.files/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 done very quickly (<10 seconds), and upon finishing you will have three output files:

    1BJU.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 1BJU.primary_residues.sh. Write this inside of it (copied from Brian's script *.fpsrescore.qsub.sh):

    grep -A 1 "range_union" 1BJU.footprint_rescore.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 > 1BJU.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 1BJU.reference.txt
    rm temp.dat

Run the script and you should have two new files:

   1BJU.primary_residues.dat
   1BJU.reference.txt 

These are our primary residues! Now we need to generate a grid for each one.

Generating the Grids