Table 2.
Key DOCK_DN parameter values used in this work.
Parameter | Description | Value |
---|---|---|
dn_sampling method | Method employed for picking fragments (exhaustive, random, graph) | random |
dn_num_random_picks | N fragments randomly selected | 20, 50 |
dn_mol_wt_cutoff_type | Molecular weight filtering method (hard, soft) | soft |
dn_upper_constraint_mol_wt | The upper limit for MW filter | 550 |
dn_lower_constraint_mol_wt | The lower limit for MW filter | 0 |
dn_mol_wt_std_dev | The standard deviation for MW filter | 35 |
dn_constraint_rot_bon | The max rotatable bonds allowed | 15 |
dn_constraint_formal_charge | Largest absolute charge of molecule | 2 |
dn_max_grow_layers | Max number of layers for growth starting from an anchor | 9 |
dn_max_root_size | Max number of new molecules allowed from any given growing molecule | 25, 50 |
dn_max_layer_size | Max number of partially grown molecules that advanced to the next layer | 25, 50 |
dn_max_current_aps | Max number of unsatisfied attachment points at any given time | 5 |
dn_max_scaffolds_per_layer | Max number of scaffolds added per layer per molecule | 1 |