<s>
AutoDock	B-Application
is	O
a	O
molecular	O
modeling	O
simulation	O
software	O
.	O
</s>
<s>
AutoDock	B-Application
4	O
is	O
available	O
under	O
the	O
GNU	B-License
General	I-License
Public	I-License
License	I-License
.	O
</s>
<s>
AutoDock	B-Application
is	O
one	O
of	O
the	O
most	O
cited	O
docking	O
software	O
applications	O
in	O
the	O
research	O
community	O
.	O
</s>
<s>
It	O
is	O
used	O
by	O
the	O
FightAIDS	B-Operating_System
@Home	I-Operating_System
and	O
OpenPandemics	O
-	O
COVID-19	O
projects	O
run	O
at	O
World	B-Operating_System
Community	I-Operating_System
Grid	I-Operating_System
,	O
to	O
search	O
for	O
antivirals	O
against	O
HIV/AIDS	O
and	O
COVID-19	O
.	O
</s>
<s>
In	O
February	O
2007	O
,	O
a	O
search	O
of	O
the	O
ISI	O
Citation	O
Index	O
showed	O
more	O
than	O
1,100	O
publications	O
had	O
been	O
cited	O
using	O
the	O
primary	O
AutoDock	B-Application
method	O
papers	O
.	O
</s>
<s>
AutoDock	B-Application
Vina	O
is	O
a	O
successor	O
of	O
AutoDock	B-Application
,	O
significantly	O
improved	O
in	O
terms	O
of	O
accuracy	O
and	O
performance	O
.	O
</s>
<s>
It	O
is	O
available	O
under	O
the	O
Apache	B-Application
license	I-Application
.	O
</s>
<s>
AutoDock	B-Application
is	O
widely	O
used	O
and	O
played	O
a	O
role	O
in	O
the	O
development	O
of	O
the	O
first	O
clinically	O
approved	O
HIV-1	O
integrase	O
inhibitor	O
by	O
Merck	O
&	O
Co	O
.	O
</s>
<s>
AutoDock	B-Application
consists	O
of	O
two	O
main	O
programs	O
:	O
</s>
<s>
AutoDock	B-Application
for	O
docking	O
of	O
the	O
ligand	O
to	O
a	O
set	O
of	O
grids	O
describing	O
the	O
target	O
protein	O
;	O
</s>
<s>
Usage	O
of	O
AutoDock	B-Application
has	O
contributed	O
to	O
the	O
discovery	O
of	O
several	O
drugs	O
,	O
including	O
HIV1	O
integrase	O
inhibitors	O
.	O
</s>
<s>
AutoDock	B-Application
runs	O
on	O
Linux	B-Application
,	O
Mac	B-Operating_System
OS	I-Operating_System
X	I-Operating_System
,	O
SGI	B-Operating_System
IRIX	I-Operating_System
,	O
and	O
Microsoft	B-Application
Windows	I-Application
.	O
</s>
<s>
It	O
is	O
available	O
as	O
a	O
package	O
in	O
several	O
Linux	B-Application
distributions	O
,	O
including	O
Debian	O
,	O
Fedora	O
,	O
and	O
Arch	O
Linux	B-Application
.	O
</s>
<s>
Compiling	O
the	O
application	O
in	O
native	O
64-bit	B-Device
mode	O
on	O
Microsoft	B-Application
Windows	I-Application
enables	O
faster	O
floating-point	O
operation	O
of	O
the	O
software	O
.	O
</s>
<s>
Improved	O
calculation	O
routines	O
using	O
OpenCL	B-Application
and	O
CUDA	B-Architecture
have	O
been	O
developed	O
by	O
the	O
AutoDock	B-Application
Scripps	O
research	O
team	O
.	O
</s>
<s>
It	O
results	O
in	O
observed	O
speedups	O
of	O
up	O
to	O
4x	O
(	O
quad-core	O
CPU	O
)	O
and	O
56x	O
(	O
GPU	O
)	O
over	O
the	O
original	O
serial	O
AutoDock	B-Application
4.2	O
(	O
Solis-Wets	O
)	O
on	O
CPU	O
.	O
</s>
<s>
The	O
CUDA	B-Architecture
version	O
was	O
developed	O
in	O
a	O
collaboration	O
between	O
the	O
Scripps	O
research	O
team	O
and	O
Nvidia	O
while	O
the	O
OpenCL	B-Application
version	O
was	O
further	O
optimized	O
with	O
support	O
from	O
the	O
IBM	O
World	B-Operating_System
Community	I-Operating_System
Grid	I-Operating_System
team	O
.	O
</s>
<s>
AutoDock	B-Application
has	O
a	O
successor	O
,	O
AutoDock	B-Application
Vina	O
,	O
which	O
has	O
an	O
improved	O
local	O
search	O
routine	O
and	O
makes	O
use	O
of	O
multicore/multi	O
-CPU	O
computer	O
setups	O
.	O
</s>
<s>
AutoDock	B-Application
Vina	O
has	O
been	O
noted	O
for	O
running	O
significantly	O
faster	O
under	O
64-bit	B-Device
Linux	B-Application
operating	I-Application
systems	I-Application
in	O
several	O
World	B-Operating_System
Community	I-Operating_System
Grid	I-Operating_System
projects	O
that	O
used	O
the	O
software	O
.	O
</s>
<s>
AutoDock	B-Application
Vina	O
is	O
currently	O
on	O
version	O
1.2	O
,	O
released	O
in	O
July	O
2021	O
.	O
</s>
<s>
As	O
an	O
open	O
source	O
project	O
,	O
AutoDock	B-Application
has	O
gained	O
several	O
third-party	O
improved	O
versions	O
such	O
as	O
:	O
</s>
<s>
Scoring	O
and	O
Minimization	O
with	O
AutoDock	B-Application
Vina	O
(	O
smina	O
)	O
is	O
a	O
fork	O
of	O
AutoDock	B-Application
Vina	O
with	O
improved	O
support	O
for	O
scoring	O
function	O
development	O
and	O
energy	O
minimization	O
.	O
</s>
<s>
Off-Target	O
Pipeline	O
allows	O
integration	O
of	O
AutoDock	B-Application
within	O
bigger	O
projects	O
.	O
</s>
<s>
Consensus	O
Scoring	O
ToolKit	O
provides	O
rescoring	O
of	O
AutoDock	B-Application
Vina	O
poses	O
with	O
multiple	O
scoring	O
functions	O
and	O
calibration	O
of	O
consensus	O
scoring	O
equations	O
.	O
</s>
<s>
VSLAB	O
is	O
a	O
VMD	B-Application
plug-in	O
that	O
allows	O
the	O
use	O
of	O
AutoDock	B-Application
directly	O
from	O
VMD	B-Application
.	O
</s>
<s>
PyRx	O
provides	O
a	O
nice	O
GUI	O
for	O
running	O
virtual	O
screening	O
with	O
AutoDock	B-Application
.	O
</s>
<s>
PyRx	O
includes	O
a	O
docking	O
wizard	O
and	O
you	O
can	O
use	O
it	O
to	O
run	O
AutoDock	B-Application
Vina	O
in	O
the	O
Cloud	O
or	O
HPC	O
cluster	O
.	O
</s>
<s>
POAP	O
is	O
a	O
shell-script-based	O
tool	O
which	O
automates	O
AutoDock	B-Application
for	O
virtual	O
screening	O
from	O
ligand	O
preparation	O
to	O
post	O
docking	O
analysis	O
.	O
</s>
<s>
VirtualFlow	O
allows	O
to	O
carry	O
out	O
ultra-large	O
virtual	O
screenings	O
on	O
computer	O
clusters	O
and	O
the	O
cloud	O
using	O
AutoDock	B-Application
Vina-based	O
docking	O
programs	O
,	O
allowing	O
to	O
routinely	O
screen	O
billions	O
of	O
compounds	O
.	O
</s>
