Skip to main content

Some NLM-NCBI services and products are experiencing heavy traffic, which may affect performance and availability. We apologize for the inconvenience and appreciate your patience. For assistance, please contact our Help Desk at info@ncbi.nlm.nih.gov.

. Author manuscript; available in PMC: 2024 Jul 25.
Published in final edited form as: J Chem Inf Model. 2023 Sep 12;63(18):5803–5822. doi: 10.1021/acs.jcim.3c01031

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
HHS Vulnerability Disclosure