Difference between revisions of "2010 DOCK tutorial with Streptavidin"
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cd /nfs/user03/username/1DF8_setup | cd /nfs/user03/username/1DF8_setup | ||
/nfs/user03/sudipto/dock6/bin/dock6 -i rigid.in -o rigid.out | /nfs/user03/sudipto/dock6/bin/dock6 -i rigid.in -o rigid.out | ||
| + | |||
| + | |||
| + | |||
| + | Now we do something similar with flexible binding: | ||
| + | vi flex.in | ||
| + | |||
| + | ligand_atom_file 1DF8.lig.mol2 | ||
| + | limit_max_ligands no | ||
| + | skip_molecule no | ||
| + | read_mol_solvation no | ||
| + | calculate_rmsd yes | ||
| + | use_rmsd_reference_mol no | ||
| + | use_database_filter no | ||
| + | orient_ligand yes | ||
| + | automated_matching yes | ||
| + | receptor_site_file selected_spheres.sph | ||
| + | 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 40 | ||
| + | pruning_use_clustering yes | ||
| + | pruning_max_orients 100 | ||
| + | pruning_clustering_cutoff 100 | ||
| + | pruning_conformer_score_cutoff 25.0 | ||
| + | use_clash_overlap no | ||
| + | write_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 grid | ||
| + | dock3.5_score_secondary no | ||
| + | continuous_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 20 | ||
| + | simplex_grow_tors_premin_iterations 20 | ||
| + | simplex_random_seed 0 | ||
| + | simplex_restraint_min no | ||
| + | atom_model all | ||
| + | vdw_defn_file vdw_AMBER_parm99.defn | ||
| + | flex_defn_file /nfs/user03/sudipto/dock6/parameters/flex.defn | ||
| + | flex_drive_file /nfs/user03/sudipto/dock6/parameters/flex_drive.tbl | ||
| + | ligand_outfile_prefix flex | ||
| + | write_orientations no | ||
| + | num_scored_conformers 5000 | ||
| + | write_conformations no | ||
| + | cluster_conformations yes | ||
| + | cluster_rmsd_threshold 2.0 | ||
| + | rank_ligands no | ||
| + | |||
| + | Now you can run this file through a .csh. We made ours like this: | ||
| + | vi dock6.flex.csh | ||
| + | |||
| + | #!/bin/csh | ||
| + | #PBS -l nodes=1:ppn=2 | ||
| + | #PBS -l walltime=01:00:00 | ||
| + | #PBS -N dock6 | ||
| + | #PBS -M user@ic.sunysb.edu | ||
| + | #PBS -j oe | ||
| + | #PBS -o pbs2.out | ||
| + | cd /nfs/user03/username/1DF8_setup | ||
| + | /nfs/user03/sudipto/dock6/bin/dock6 -i flex.in -o flex.out | ||
==Docking Results== | ==Docking Results== | ||
Revision as of 18:47, 20 February 2010
Contents
About DOCK
DOCK was developed by Irwin D. "Tack" Kuntz, Jr., PhD and colleagues at UCSF. Please see the webpage at UCSF DOCK.
DOCK is a molecular docking program used in drug discovery. This program, given a protein active site and a small molecule, tries to predict the correct binding mode of the small molecule in the active site, and the associated binding energy. Small molecules with highly favorable binding energies could be new drug leads. This makes DOCK a valuable drug discovery tool. DOCK is typically used to screen massive libraries of millions of compounds against a protein to isolate potential drug leads. These leads are then further studied, and could eventually result in a new, marketable drug.
About Streptavidin & Biotin
Streptavidin is a tetrameric prokaryoke protein that binds the co-enzyme biotin with an extremely high affinity. The streptavidin monomer is composed of eight antiparallel beta-strands which folds to give a beta barrel tertiary structure. A biotin binding-site is located at one end of each β-barrel, which has a high affinity as well as a high avidity for biotin. Four identical streptavidin monomers associate to give streptavidin’s tetrameric quaternary structure. The biotin binding-site in each barrel consists of residues from the interior of the barrel, together with a conserved Trp120 from neighbouring subunit. In this way, each subunit contributes to the binding site on the neighboring subunit, and so the tetramer can also be considered a dimer of functional dimers.
Biotin is a water soluble B-vitamin complex which is composed of an ureido (tetrahydroimidizalone) ring fused with a tetrahydrothiophene ring. It is a co-enzyme that is required in the metabolism of fatty acids and leucine. It is also involved in gluconeogenisis.
Downloading the PDB complex (1DF8)
Download the neuraminidase file from here into your working directory. To get the monomer, download using the blue file arrow icon. Choose biological unit gz under download files folder at the left side. In that way you can downlad a biological gz file. If you download it by using "fetch by ID" in Chimera, you can only download a pdb gz file.
If the pdb gz file is downloaded the monomeric structure of neuraminidase with the bound ligand is seen.
However if the biological gz file is downloaded a tetramer complex of neuraminidase is seen.
When docking, we will only choose a monomer of the whole protein and its ligands instead of the whole tetramer. And it will be painful if you follow the procedure below, use vi to prepare the enzyme and ligand. Because you need to make sure the ligand you extract from the whole pdb files is right the one that match the monomer you've chosen.
Preparing the Enzyme and Ligand in Chimera
To delete the water molecules, etc. go to tools->struc. edit--> dock prep. Check all boxes and click ok. Save as 1DF8.dockprep.mol2 To separate the ligand: select--->residue-->BTN. Then go to actions-->atoms--->delete Save file: 1DF8.receptor.mol2 Select--->chemistry-->element-->H and delete. Save as PDB file 1DF8.receptor.noH.pdb close and open dockprep file again. select protein and delete. Now have ligand only. Save as 1DF8.lig.mol2
Generation of Enzyme Surface, Spheres, and Grid for DOCK
Enzyme Surface
To generate an enzyme surface, first open the receptor pdb file with the hydrogen atoms removed (1DF8.rec.noH.pdb). Next, go to Actions -> Surface -> Show.
Recent versions of Chimera include a Write DMS tool that facilitates calculation of the molecular surface. Go to Tools -> Structure Editing -> Write DMS. Save the surface as 1DF8.rec.dms.
The Write DMS algorithm will "roll" a small probe (default radius = 1.4 Angstroms) over the surface of the enzyme and calculate the surface normal at each point. Note that this can also be accomplished with a separate dms program, as described in DOCK tutorials from previous years. DMS (dot molecular surface) files are subsequently used as input for sphgen.
Spheres
To generate spheres file, we need to use command line program called sphgen. To run the sphgen, we need a input file named INSPH. The content of INSPH is like this
1DF8_receptor.dms R X 0.0 4.0 1.4 1DF8_receptor.sph
1DF8_receptor.ms is the surface file we got from the previous step. (Change the file name to what you named it before). 1DF8_receptor.sph is the spheres file we want to generate in this step.
Use this command to generate spheres file
sphgen -i INSPH -o OUTSPH
You should get the OUTSPH similar to this
density type = X reading 1DF8_receptor.dms type R # of atoms = 881 # of surf pts = 10771 finding spheres for 1DF8_receptor.dms dotlim = 0.000 radmax = 4.000 Minimum radius of acceptable spheres? 1.4000000 output to 1DF8_receptor.sph clustering is complete 27 clusters
You can open the spheres file (1DF8_receptor.sph). There are over 700 atoms in this file. However, we're only interested in docking the ligand into the active site. To get better efficiency, we can select those sphere atoms in the active site by using sphere_selector command.
sphere_selector 1DF8_receptor.sph 1DF8_ligand.mol2 10.0
Where 1DF8_ligand is the ligand file. 10.0 is the distance cutoff. You should get a file called selected_spheres.sph. You can open it. The number of atoms is drop down to 47.
Grid
Running DOCK
You can run dock with either a rigid or flexible ligand. For either one, you need to creat an input file.
Lets start with a rigid ligand. We need to first make the input file by typing in:
vi rigid.in
The rigid.in file is:
ligand_atom_file 1DF8.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol no use_database_filter no orient_ligand yes automated_matching yes receptor_site_file selected_spheres.sph max_orientations 1000 critical_points no chemical_matching no use_ligand_spheres 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 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 grid dock3.5_score_secondary no continuous_score_secondary no gbsa_zou_score_secondary no gbsa_hawkins_score_secondary no amber_score_secondary no minimize_ligand yes simplex_max_iterations 1000 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 simplex_restraint_min no atom_model all vdw_defn_file vdw_AMBER_parm99.defn flex_defn_file /nfs/user03/sudipto/dock6/parameters/flex.defn flex_drive_file /nfs/user03/sudipto/dock6/parameters/flex_drive.tbl ligand_outfile_prefix rigid write_orientations no num_scored_conformers 5000 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
Note-The vdw_defn_file was in my directory. The flex_defn_file and flex_drive_file files were in sudiptos directory
Now you can run this file through a .csh. We made ours like this:
vi dock6.rigid.csh
#!/bin/csh #PBS -l nodes=1:ppn=2 #PBS -l walltime=01:00:00 #PBS -N dock6 #PBS -M user@ic.sunysb.edu #PBS -j oe #PBS -o pbs.out cd /nfs/user03/username/1DF8_setup /nfs/user03/sudipto/dock6/bin/dock6 -i rigid.in -o rigid.out
Now we do something similar with flexible binding:
vi flex.in
ligand_atom_file 1DF8.lig.mol2 limit_max_ligands no skip_molecule no read_mol_solvation no calculate_rmsd yes use_rmsd_reference_mol no use_database_filter no orient_ligand yes automated_matching yes receptor_site_file selected_spheres.sph 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 40 pruning_use_clustering yes pruning_max_orients 100 pruning_clustering_cutoff 100 pruning_conformer_score_cutoff 25.0 use_clash_overlap no write_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 grid dock3.5_score_secondary no continuous_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 20 simplex_grow_tors_premin_iterations 20 simplex_random_seed 0 simplex_restraint_min no atom_model all vdw_defn_file vdw_AMBER_parm99.defn flex_defn_file /nfs/user03/sudipto/dock6/parameters/flex.defn flex_drive_file /nfs/user03/sudipto/dock6/parameters/flex_drive.tbl ligand_outfile_prefix flex write_orientations no num_scored_conformers 5000 write_conformations no cluster_conformations yes cluster_rmsd_threshold 2.0 rank_ligands no
Now you can run this file through a .csh. We made ours like this:
vi dock6.flex.csh
#!/bin/csh #PBS -l nodes=1:ppn=2 #PBS -l walltime=01:00:00 #PBS -N dock6 #PBS -M user@ic.sunysb.edu #PBS -j oe #PBS -o pbs2.out cd /nfs/user03/username/1DF8_setup /nfs/user03/sudipto/dock6/bin/dock6 -i flex.in -o flex.out
