[Dock-fans] some question of rigid socre and time expened.
Trent E. Balius
tbalius at aol.com
Tue Jul 23 06:40:54 PDT 2013
I am also sending this to the dock-fans mailing list.
I understand that you are performing docking with rigid ligand:
This is a large approximation, the starting geometry of the ligands are
likely not the geometries that will fit well in the pocket. I believe
that if you allow for ligand flexibility that this will help your
There are several parameters that you may wish to adjust to get better
These changes might effect accuracy. I would suggest changing the
following two parameters:
See the following posting for more discussion on speed.
I hope this helps,
---- Original Message ----
From: LiLei <2012222040093 at stu.scu.edu.cn>
To: tbalius <tbalius at aol.com>
Sent: Sun, Jul 21, 2013 11:33 am
Subject: some question of rigid socre and time expened.
I,m a postgraduate from china and want to use dock6.6 for screening
some inhibitors of our intereast target protein and I'm so sorry to
trouble you again.
Previously, I have made some enrichment tests with rigid method.After
my enrichment tests finished,almost all the AUC% were lower than that
from DUD-E website.
So I want to know if other score function is better than rigid score
for this purpose?
And i find that when use rigid method docked some ligand into target
protien,the total elapsed time was 248 seconds ,some even more than 300
seconds. My ligand library were more than 120,000 ligands so the time
expended will very large.
some information of dock.out as follows:
Initializing Library File Routines...
Initializing Orienting Routines...
Read in 54 spheres for orienting.
Initializing Grid Score Routines...
Reading the energy grid from grid.nrg
Done reading the energy grid.
Reading the grid box quantifiers from grid.bmp
size = 839800
spacing = 0.3
origin = -5.795,-27.082,6.1185
span = 95,85,104
Done reading the grid box quantifiers.
VERBOSE MOLECULE STATS
Number of heavy atoms = 29
Number of rotatable bonds = 5
Formal Charge = 0.00
Molecular Weight = 407.47
Heavy Atoms = 29
VERBOSE ORIENTING STATS :
Orienting 29 anchor heavy atom centers
Sphere Center Matching Parameters:
tolerance: 0.25; dist_min: 2; min_nodes: 3; max_nodes: 10
Num of cliques generated: 1622
min residual: 0.0108
median residual: 0.1992
max residual: 0.2500
mean residual: 0.1902
std residual: 0.0464
min nodes: 3
max nodes: 4
mean nodes: 3.0012
Elapsed time for docking: 248 seconds
and my dock.in parameters as follows:
My box size was 8 angstrom.
So how to change the parameters of dock.in and can increase
efficiency,because i have changed some parameters but can not get
better.May i get your help when you have time.
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