Table S3
Docking parameters used for docking using seven programs in this work.
Program
Program
type
Scoring
function
AutoDock
Genetic
Algorithm
AutoDock
score
Scoring
function
type
Force Field/
Empirical
Program
source
Standalone
Docking parameters
-
eHiTS
Fragment
-based
eHiTS
score
Knowledgebased
Standalone
-
-
-
-
FlexX
Fragment
-based
FlexX
score
Empirical
Sybyl/
Standalone
-
Glide
MonteCarlo
sampling
GlideScor
e SP
Empirical
Maestro
-
GOLD
Genetic
Algorithm
GoldScore
Force Field
Standalone
-
Population size 150,
Number of genetic operations
27,000
Elitism equal 1
Number of separate
populations equal 1
Active site based on ligand
position
Number of cavity nodes =
200-600
Number of candidates to be
selected as cavity node center
= 200-15000
Limit on the number of
LigNode positions in whole
cavity = 250
Limit on the number of poses
for first step GraphMatch =
1000
Increament of the number of
poses in each step of
GraphMatch = 600
Ligand torsion angle model –
MIMUBA
Automatically chosen base
fragment
Rings flexibility turn off
Molecule undergo flexible
optimization after ligand is
recreated
Max. number of atoms in
ligand 200
Max. number of rotatable
bonds 35.
Scoring function in SP
(Standard precision) mode
Population size 100
Selective pressure 1.1
Number of isolated
populations 3
Number of genetic operations
30000
LigandFit
ShapeComplem
entary
LigScore
Empirical
Cerius2/
Discovery
Studio
-
-
Surflex
Fragment
-based
Surflex
score
Empirical
Sybyl
-
-
-
The Monte Carlo parameters
depended on the number of
rotatable bonds in docked
molecules. For two rotatable
bonds the maximal number of
trials to perform and the
number of consecutive failed
trials was 1000 and 240
respectively. If molecule has
10 of those bonds the number
grown to 20000 and 5000
The number of poses that
undergo final rigid
minimization was set to 100
Protomol was generated
based on ligand placement
with threshold values set to
0.5
No additional starting
conformations were
generated
Ring flexibility was turn off
Total number of ten poses
was saved to output file per
each ligan