View source for 2012 DOCK tutorial with Streptavidin

For additional Rizzo Lab tutorials see [[DOCK Tutorials]].

==I. Introduction==

===DOCK===

DOCK was developed by Irwin D. "Tack" Kuntz, Jr., PhD and colleagues at UCSF.  Please see the webpage at [http://dock.compbio.ucsf.edu/ 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. DOCK is works well as a screening procedure for generating leads, but not nearly as well for optimization of those leads. Original DOCK used only rigid body docking, DOCK 4.0, however, introduced flexible ligand docking by either a)incremental construction or b)random search. 

Incremental construction (aka anchor and grow) could be roughly described by a three step process:
1) rigid portion of ligand (anchor) is docked by geometrical methods
2) non-rigid segments added; energy minimized
3) the resulting configurations are 'pruned' and energy re-minimized, yielding the docked configurations

Random search method involves docking random conformations of ligand as independent rigid objects. The number of conformations allowed per rotatable bond is arbitrary and user controlled. The receptor is always held rigid in DOCK 4.0.

===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.

==II. Preparing the Enzyme and Ligand in Chimera==

===Downloading the PDB complex===

===DOCKprep in Chimera===

==III. Generation of Enzyme Surface and Spheres==


===Enzyme Surface===


===Spheres===

==IV. Generation of Box and Grid==

===Box===

===Grid===

==V. Docking a Single Molecule==

===Rigid Docking Protocol===

The rigid.in file is: 

 ligand_atom_file                                             1DF8.ligand.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                                               flex.defn
 flex_drive_file                                              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 



===Flexible Docking Protocol===

The flex.in file is:

 ligand_atom_file                                             1DF8.ligand.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                                               flex.defn
 flex_drive_file                                              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

===Docking Results===

==VI. Virtual Screening==

Sample flex virtual screening input file

 ligand_atom_file                       3_t60.mol2
 limit_max_ligands                      no
 skip_molecule                          no
 read_mol_solvation                     no
 calculate_rmsd                         no
 use_database_filter                    yes
 dbfilter_max_heavy_atoms               999
 dbfilter_min_heavy_atoms               0
 dbfilter_max_rot_bonds                 999
 dbfilter_min_rot_bonds                 0
 dbfilter_max_molwt                     9999.0
 dbfilter_min_molwt                     0.0
 dbfilter_max_formal_charge             10.0
 dbfilter_min_formal_charge             -10.0
 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                        5
 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          1000
 simplex_grow_max_iterations            20
 simplex_grow_tors_premin_iterations    0
 simplex_random_seed                    0
 simplex_restraint_min                  no
 atom_model                             all
 vdw_defn_file                          vdw.defn
 flex_defn_file                         flex.defn
 flex_drive_file                        flex_drive.tbl
 ligand_outfile_prefix                  vs
 write_orientations                     no
 num_scored_conformers                  1
 rank_ligands                           yes
 max_ranked_ligands                     20000


==VII. Running DOCK and Virtual Screen on Seawulf==