Docking binding energy (mean lowest) values and the number of members of each cluster
Compound 11 (NMDS-11)
Cluster Rank
1
2
3
4
5
Lowest Binding
energy
-8.68
-8.57
-8.30
-8.02
-7.97
Run
2
5
8
4
1
Mean binding
energy
-8.68
-8.23
-8.03
-8.02
-7.97
Number in cluster
Mean binding
energy
-7.97
-7.55
-6.82
-7.13
-6.58
Number in cluster
1
3
4
1
1
Compound 9 (NMDS-9)
Cluster Rank
1
2
3
4
5
Lowest Binding
energy
-8.31
-7.62
-7.37
-7.13
-6.58
Run
8
5
9
2
6
3
2
3
1
1
Template DPF for nmds 9
outlev 1
intelec
seed pid time
ligand_types A C HD OA N
fld 1sfm_rigid_noligand.maps.fld
map 1sfm_rigid_noligand.A.map
map 1sfm_rigid_noligand.C.map
map 1sfm_rigid_noligand.HD.map
map 1sfm_rigid_noligand.OA.map
map 1sfm_rigid_noligand.N.map
elecmap 1sfm_rigid_noligand.e.map
desolvmap 1sfm_rigid_noligand.d.map
move NMDS-9.pdbqt
flexres 1sfm_flex_noligand.pdbqt
about 0.5356 0.796 0.0194
tran0 random
quat0 random
ndihe 4
dihe0 random
tstep 2.0
qstep 50.0
dstep 50.0
torsdof 4 0.274000
coefficient
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
diagnostic output level
calculate internal electrostatics
seeds for random generator
atoms types in ligand
grid_data_file
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
electrostatics map
desolvation map
small molecule
file containing flexible residues
small molecule center
initial coordinates/A or random
initial quaternion
number of active torsions
initial dihedrals (relative) or random
translation step/A
quaternion step/deg
torsion step/deg
torsional degrees of freedom and
rmstol 2.0
extnrg 1000.0
e0max 0.0 10000
retries
ga_pop_size 150
ga_num_evals 250000
ga_num_generations 27000
ga_elitism 1
to next generation
ga_mutation_rate 0.02
ga_crossover_rate 0.8
ga_window_size 10
ga_cauchy_alpha 0.0
ga_cauchy_beta 1.0
set_ga
sw_max_its 300
search
sw_max_succ 4
rho
sw_max_fail 4
rho
sw_rho 1.0
sw_lb_rho 0.01
ls_search_freq 0.06
on individual
set_sw1
compute_unbound_extended
ga_run 10
analysis
# cluster_tolerance/A
# external grid energy
# max initial energy; max number of
#
#
#
#
number of individuals in population
maximum number of energy evaluations
maximum number of generations
number of top individuals to survive
#
#
#
#
#
#
#
rate of gene mutation
rate of crossover
Alpha parameter of Cauchy distribution
Beta parameter Cauchy distribution
set the above parameters for GA or LGA
iterations of Solis & Wets local
# consecutive successes before changing
# consecutive failures before changing
# size of local search space to sample
# lower bound on rho
# probability of performing local search
#
#
#
#
set the
compute
do this
perform
above Solis & Wets parameters
extended ligand energy
many hybrid GA-LS runs
a ranked cluster analysis
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
diagnostic output level
calculate internal electrostatics
seeds for random generator
atoms types in ligand
grid_data_file
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
electrostatics map
desolvation map
small molecule
file containing flexible residues
small molecule center
initial coordinates/A or random
initial quaternion
number of active torsions
initial dihedrals (relative) or random
translation step/A
quaternion step/deg
torsion step/deg
Template DPF for nmds 11
outlev 1
intelec
seed pid time
ligand_types A C OA N HD
fld 1sfm_rigid_noligand.maps.fld
map 1sfm_rigid_noligand.A.map
map 1sfm_rigid_noligand.C.map
map 1sfm_rigid_noligand.OA.map
map 1sfm_rigid_noligand.N.map
map 1sfm_rigid_noligand.HD.map
elecmap 1sfm_rigid_noligand.e.map
desolvmap 1sfm_rigid_noligand.d.map
move NMDS-11.pdbqt
flexres 1sfm_flex_noligand.pdbqt
about 0.6467 0.3439 0.1506
tran0 random
quat0 random
ndihe 1
dihe0 random
tstep 2.0
qstep 50.0
dstep 50.0
torsdof 1 0.274000
coefficient
rmstol 2.0
extnrg 1000.0
e0max 0.0 10000
retries
ga_pop_size 150
ga_num_evals 250000
ga_num_generations 27000
ga_elitism 1
to next generation
ga_mutation_rate 0.02
ga_crossover_rate 0.8
ga_window_size 10
ga_cauchy_alpha 0.0
ga_cauchy_beta 1.0
set_ga
sw_max_its 300
search
sw_max_succ 4
rho
sw_max_fail 4
rho
sw_rho 1.0
sw_lb_rho 0.01
ls_search_freq 0.06
on individual
set_sw1
compute_unbound_extended
ga_run 10
analysis
# torsional degrees of freedom and
# cluster_tolerance/A
# external grid energy
# max initial energy; max number of
#
#
#
#
number of individuals in population
maximum number of energy evaluations
maximum number of generations
number of top individuals to survive
#
#
#
#
#
#
#
rate of gene mutation
rate of crossover
Alpha parameter of Cauchy distribution
Beta parameter Cauchy distribution
set the above parameters for GA or LGA
iterations of Solis & Wets local
# consecutive successes before changing
# consecutive failures before changing
# size of local search space to sample
# lower bound on rho
# probability of performing local search
#
#
#
#
set the
compute
do this
perform
above Solis & Wets parameters
extended ligand energy
many hybrid GA-LS runs
a ranked cluster analysis
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
num.grid points in xyz
grid_data_file
spacing(A)
receptor atom types
ligand atom types
macromolecule
xyz-coordinates or auto
store minimum energy w/in rad(A)
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
atom-specific affinity map
electrostatic potential map
desolvation potential map
<0, AD4 distance-dep.diel;>0, constant
Template GPF
npts 78 72 68
gridfld 1sfm_rigid_noligand.maps.fld
spacing 0.375
receptor_types A C HD N OA SA
ligand_types A C HD N NA OA SA
receptor 1sfm_rigid_noligand.pdbqt
gridcenter 66.7 15.8 20.0
smooth 0.5
map 1sfm_rigid_noligand.A.map
map 1sfm_rigid_noligand.C.map
map 1sfm_rigid_noligand.HD.map
map 1sfm_rigid_noligand.N.map
map 1sfm_rigid_noligand.NA.map
map 1sfm_rigid_noligand.OA.map
map 1sfm_rigid_noligand.SA.map
elecmap 1sfm_rigid_noligand.e.map
dsolvmap 1sfm_rigid_noligand.d.map
dielectric -0.1465