Joe and Brian de novo stuff
From Rizzo_Lab
Revision as of 17:19, 19 September 2015 by Stonybrook (talk | contribs) (→The input file we should be using:)
This is Joe and Brian's secret wiki page for coordinating notes on the de novo project.
Contents
- 1 Version of the code on cluster that we should be using:
- 2 List of SB2012 systems that we will use for tests:
- 3 Experiments run with the current binary:
- 4 List of features that we definitely want for the release:
- 5 List of features that would be nice to have, but not necessary for release:
- 6 The input file we should be using:
Version of the code on cluster that we should be using:
/sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper /sbhome1/wjallen/work/build/dock.6.7_2015-02-17.denovo_paper/src/dock/dock6
We will probably do a merge after 6.8 is released. Brian: If you have any edits to the code, do a diff and e-mail me the results. I will merge it into my branch and confirm with you that I made that change.
List of SB2012 systems that we will use for tests:
For now, let's use 5-15 rotatable bonds inclusive; total = 709 systems. [Joe]: I like this set because it represents "drug-like" size molecules, and they should not be too easy / too hard.
{5RB = 107; 6RB = 96; 7RB = 103; 8RB = 75; 9RB = 66; 10RB = 75; 11RB = 57; 12RB = 41; 13RB = 38; 14RB = 26; 15RB = 25}
Experiments run with the current binary:
| TAN_CUT | UNMAT_NUM | MAT_RMSD | MAX_LAY | MAX_APS | MAX_ROOT_SZ | MAX_LAY_SZ | RES_MIN | SYS | LIB | SCR_FN_GR | NOTES |
| 1.0 | 0 | 2.0 | 9 | 7 | 50 | 50 | no | 5-15 | focused | des_grid | 005hhh |
| 1.0 | 6 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM6 |
| 1.0 | 4 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM4 |
| 1.0 | 2 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpUM2 |
| 1.0 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005hh |
| 1.0 | 0 | 2.0 | 9 | 3 | 50 | 50 | no | 5-15 | focused | des_grid | 005h |
| 1.0 | 0 | 2.0 | 7 | 7 | 50 | 50 | no | 5-15 | focused | des_grid | 005ggg |
| 1.0 | 0 | 2.0 | 7 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005gg |
| 1.0 | 0 | 2.0 | 7 | 3 | 50 | 50 | no | 5-15 | focused | des_grid | 005g |
| 1.0 | 0 | 2.0 | 7 | 3 | 50 | 50 | yes | 5-15 | focused | des_grid | 005i |
| 0.95 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan095 |
| 0.90 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan090 |
| 0.85 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan085 |
| 0.80 | 0 | 2.0 | 9 | 5 | 50 | 50 | no | 5-15 | focused | des_grid | 005_hpTan080 |
List of features that we definitely want for the release:
| Task | Owner | Complete? |
|---|---|---|
| Put molecular properties (RB, MW, etc) in mol2 header | WJA | |
| Put ensemble properties (RB, MW, etc) output stream at the end of each layer | WJA | |
| check formal charge prune | BCF | |
| combination of horizontal pruning metrics | X | |
| growth trees | X | |
| something | X | |
| something | X |
List of features that would be nice to have, but not necessary for release:
- Stereo Centers
- Volume Overlap
- Capping Groups (H, CH3, Halogen)
- Figure out a way to speed up the fingerprint calculations
The input file we should be using:
Note: these are not all the current default parameter. I am going to update the version of the code above so that everything below is the current default.
conformer_search_type denovo dn_fraglib_scaffold_file fraglib_scaffold.mol2 dn_fraglib_linker_file fraglib_linker.mol2 dn_fraglib_sidechain_file fraglib_sidechain.mol2 dn_user_specified_anchor yes dn_fraglib_anchor_file fraglib_anchor.mol2 dn_use_torenv_table yes dn_torenv_table torenv_table.dat dn_sampling_method graph dn_graph_starting_points 10 dn_graph_breadth 5 dn_graph_depth 2 dn_graph_temperature 100.0 dn_pruning_conformer_score_cutoff 100.0 dn_torsion_rmsd_cutoff 0.5 dn_constraint_mol_wt 1000.0 dn_constraint_rot_bon 15 dn_constraint_formal_charge 2.0 dn_constraint_charge_groups 4 dn_tanimoto_cutoff 0.7 dn_heur_unmatched_num 5 dn_heur_matched_rmsd 2.0 dn_max_grow_layers 7 dn_max_current_aps 5 dn_max_root_size 50 dn_max_layer_size 50 dn_write_checkpoints yes dn_write_orients no dn_write_growth_trees no dn_output_prefix output use_internal_energy yes internal_energy_rep_exp 12 use_database_filter no orient_ligand yes automated_matching yes receptor_site_file receptor.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 grid multigrid_score_secondary no dock3.5_score_secondary no continuous_score_secondary no footprint_similarity_score_secondary no ph4_score_secondary no 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 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 vdw.defn flex_defn_file flex.defn flex_drive_file flex_drive.tbl
