Table 2.

Key DOCK6 searching parameters employed in this work.

Parameter	Description	Values Used
dn_sampling_methoda	Fragment search methods available (random, graph, exhaustive, isoswap)	random, exhaustive, isoswap
dn_num_random_picks	N fragments randomly selected for random	20
dn_num_iso_head_picks	N fragments randomly selected for isoswap	20
dn_iso_pick_meth	TAIL fragment selection method for isoswap (top_rank, random, worst_rank)	top_rank
dn_iso_skip	Skip TAIL attempts if HEAD frag fails to attach	yes
dn_num_iso_picks	N TAIL fragments randomly selected	20, 3446
dn_random_root_selection	Randomly select molecules propagated to next layer	no
dn_mol_wt_cutoff_type	Molecular weight filtering method (hard, soft)	soft
dn_upper_constraint_mol_wt	Upper limit for MW filter	550
dn_lower_constraint_mol_wt	Lower limit for MW filter	0
dn_mol_wt_std_dev	Standard deviation for MW filter	35
dn_constraint_rot_bon	Max allowed number of rotatable bonds (#ROT)	15
dn_constraint_formal_charge	Max allowed formal charge of molecule (FC)	2
dn_heur_matched_rmsd	Max RMSD of matching heavy atoms of molecules	2.0
dn_max_grow_layersb	Max N of layers for growth starting from an anchor	9, 1
dn_max_root_size	Max N of partially grown molecules passed to next layer	25
dn_max_layer_size	Max N of molecules allowed from a given growing root	25
dn_max_successful_att_per_root	Max N of successful attachments allowed per root	50,000

^a,bLead refinement employed exhaustive searching method with 1 growth layer.