<s>
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
a	O
volunteer	B-Operating_System
computing	I-Operating_System
project	O
researching	O
protein	O
structure	O
prediction	O
on	O
the	O
Berkeley	B-Operating_System
Open	I-Operating_System
Infrastructure	I-Operating_System
for	I-Operating_System
Network	I-Operating_System
Computing	I-Operating_System
(	O
BOINC	B-Operating_System
)	O
platform	O
,	O
run	O
by	O
the	O
Baker	O
laboratory	O
at	O
the	O
University	O
of	O
Washington	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
aims	O
to	O
predict	O
protein	O
–	O
protein	O
docking	O
and	O
design	O
new	O
proteins	O
with	O
the	O
help	O
of	O
about	O
fifty-five	O
thousand	O
active	O
volunteered	O
computers	O
processing	O
at	O
over	O
487,946	O
GigaFLOPS	O
on	O
average	O
as	O
of	O
September	O
19	O
,	O
2020	O
.	O
</s>
<s>
Foldit	B-Language
,	O
a	O
Rosetta	B-Operating_System
@home	I-Operating_System
videogame	O
,	O
aims	O
to	O
reach	O
these	O
goals	O
with	O
a	O
crowdsourcing	O
approach	O
.	O
</s>
<s>
Though	O
much	O
of	O
the	O
project	O
is	O
oriented	O
toward	O
basic	O
research	O
to	O
improve	O
the	O
accuracy	O
and	O
robustness	O
of	O
proteomics	O
methods	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
also	O
does	O
applied	O
research	O
on	O
malaria	O
,	O
Alzheimer	O
's	O
disease	O
,	O
and	O
other	O
pathologies	O
.	O
</s>
<s>
Like	O
all	O
BOINC	B-Operating_System
projects	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
uses	O
idle	O
computer	O
processing	O
resources	O
from	O
volunteers	O
 '	O
computers	O
to	O
perform	O
calculations	O
on	O
individual	O
workunits	B-Operating_System
.	O
</s>
<s>
Completed	O
results	O
are	O
sent	O
to	O
a	O
central	O
project	O
server	B-Application
where	O
they	O
are	O
validated	O
and	O
assimilated	O
into	O
project	O
databases	O
.	O
</s>
<s>
The	O
project	O
is	O
cross-platform	B-Operating_System
,	O
and	O
runs	O
on	O
a	O
wide	O
variety	O
of	O
hardware	O
configurations	O
.	O
</s>
<s>
Users	O
can	O
view	O
the	O
progress	O
of	O
their	O
individual	O
protein	O
structure	O
prediction	O
on	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
screensaver	B-General_Concept
.	O
</s>
<s>
In	O
addition	O
to	O
disease-related	O
research	O
,	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
network	O
serves	O
as	O
a	O
testing	O
framework	O
for	O
new	O
methods	O
in	O
structural	O
bioinformatics	O
.	O
</s>
<s>
Such	O
methods	O
are	O
then	O
used	O
in	O
other	O
Rosetta-based	O
applications	O
,	O
like	O
RosettaDock	O
or	O
the	O
Human	B-Operating_System
Proteome	I-Operating_System
Folding	I-Operating_System
Project	I-Operating_System
and	O
the	O
Microbiome	O
Immunity	O
Project	O
,	O
after	O
being	O
sufficiently	O
developed	O
and	O
proven	O
stable	O
on	O
home	O
's	O
large	O
and	O
diverse	O
set	O
of	O
volunteer	O
computers	O
.	O
</s>
<s>
Two	O
especially	O
important	O
tests	O
for	O
the	O
new	O
methods	O
developed	O
in	O
Rosetta	B-Operating_System
@home	I-Operating_System
are	O
the	O
Critical	O
Assessment	O
of	O
Techniques	O
for	O
Protein	O
Structure	O
Prediction	O
(	O
CASP	O
)	O
and	O
Critical	O
Assessment	O
of	O
Prediction	O
of	O
Interactions	O
(	O
CAPRI	B-Application
)	O
experiments	O
,	O
biennial	O
experiments	O
which	O
evaluate	O
the	O
state	O
of	O
the	O
art	O
in	O
protein	O
structure	O
prediction	O
and	O
protein	O
–	O
protein	O
docking	O
prediction	O
,	O
respectively	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
consistently	O
ranks	O
among	O
the	O
foremost	O
docking	O
predictors	O
,	O
and	O
is	O
one	O
of	O
the	O
best	O
tertiary	O
structure	O
predictors	O
available	O
.	O
</s>
<s>
With	O
an	O
influx	O
of	O
new	O
users	O
looking	O
to	O
participate	O
in	O
the	O
fight	O
against	O
the	O
COVID-19	O
pandemic	O
,	O
caused	O
by	O
SARS-CoV-2	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
has	O
increased	O
its	O
computing	O
power	O
up	O
to	O
1.7	O
PetaFlops	O
as	O
of	O
March	O
28	O
,	O
2020	O
.	O
</s>
<s>
On	O
September	O
9	O
,	O
2020	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
researchers	O
published	O
a	O
paper	O
describing	O
10	O
potent	O
antiviral	O
candidates	O
against	O
SARS-CoV-2	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
contributed	O
to	O
this	O
research	O
and	O
these	O
antiviral	O
candidates	O
are	O
heading	O
towards	O
Phase	O
1	O
clinical	O
trials	O
,	O
which	O
may	O
begin	O
in	O
early	O
2022	O
.	O
</s>
<s>
According	O
to	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
team	O
,	O
Rosetta	O
volunteers	O
contributed	O
to	O
the	O
development	O
of	O
a	O
nanoparticle	O
vaccine	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
played	O
a	O
role	O
in	O
the	O
development	O
of	O
NL-201	O
and	O
contributed	O
with	O
"	O
forward	O
folding	O
"	O
experiments	O
that	O
helped	O
validate	O
protein	O
designs	O
.	O
</s>
<s>
The	O
Rosetta	B-Operating_System
@home	I-Operating_System
application	O
and	O
the	O
BOINC	B-Operating_System
volunteer	B-Operating_System
computing	I-Operating_System
platform	O
are	O
available	O
for	O
the	O
operating	B-General_Concept
systems	I-General_Concept
Windows	B-Application
,	O
Linux	B-Application
,	O
and	O
macOS	B-Application
;	O
BOINC	B-Operating_System
also	O
runs	O
on	O
several	O
others	O
,	O
e.g.	O
,	O
FreeBSD	O
.	O
</s>
<s>
Participation	O
in	O
Rosetta	B-Operating_System
@home	I-Operating_System
requires	O
a	O
central	B-General_Concept
processing	I-General_Concept
unit	I-General_Concept
(	O
CPU	O
)	O
with	O
a	O
clock	O
speed	O
of	O
at	O
least	O
500MHz	O
,	O
200megabytes	O
of	O
free	O
disk	B-Device
space	I-Device
,	O
512megabytes	O
of	O
physical	O
memory	O
,	O
and	O
Internet	O
connectivity	O
.	O
</s>
<s>
The	O
current	O
recommended	O
BOINC	B-Operating_System
program	O
version	O
is	O
7.6.22	O
.	O
</s>
<s>
Standard	O
Hypertext	B-Protocol
Transfer	I-Protocol
Protocol	I-Protocol
(	O
HTTP	B-Protocol
)	O
(	O
port	B-Protocol
80	O
)	O
is	O
used	O
for	O
communication	O
between	O
the	O
user	O
's	O
BOINC	B-Operating_System
client	O
and	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
servers	O
at	O
the	O
University	O
of	O
Washington	O
;	O
HTTPS	B-Protocol
(	O
port	B-Protocol
443	O
)	O
is	O
used	O
during	O
password	O
exchange	O
.	O
</s>
<s>
Remote	O
and	O
local	O
control	O
of	O
the	O
BOINC	B-Operating_System
client	O
use	O
port	B-Protocol
31416	O
and	O
port	B-Protocol
1043	O
,	O
which	O
might	O
need	O
to	O
be	O
specifically	O
unblocked	O
if	O
they	O
are	O
behind	O
a	O
firewall	B-Application
.	O
</s>
<s>
Workunits	B-Operating_System
containing	O
data	O
on	O
individual	O
proteins	O
are	O
distributed	O
from	O
servers	O
located	O
in	O
the	O
Baker	O
lab	O
at	O
the	O
University	O
of	O
Washington	O
to	O
volunteers	O
 '	O
computers	O
,	O
which	O
then	O
calculate	O
a	O
structure	O
prediction	O
for	O
the	O
assigned	O
protein	O
.	O
</s>
<s>
To	O
avoid	O
duplicate	O
structure	O
predictions	O
on	O
a	O
given	O
protein	O
,	O
each	O
workunit	B-Operating_System
is	O
initialized	O
with	O
a	O
random	B-Algorithm
seed	I-Algorithm
number	O
.	O
</s>
<s>
Protein	O
structure	O
predictions	O
from	O
Rosetta	B-Operating_System
@home	I-Operating_System
are	O
approximations	O
of	O
a	O
global	O
minimum	O
in	O
a	O
given	O
protein	O
's	O
energy	O
landscape	O
.	O
</s>
<s>
A	O
primary	O
feature	O
of	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
graphical	B-Application
user	I-Application
interface	I-Application
(	O
GUI	B-Application
)	O
is	O
a	O
screensaver	B-General_Concept
which	O
shows	O
a	O
current	O
workunit	B-Operating_System
's	O
progress	O
during	O
the	O
simulated	O
protein	O
folding	O
process	O
.	O
</s>
<s>
In	O
the	O
upper-left	O
of	O
the	O
current	O
screensaver	B-General_Concept
,	O
the	O
target	O
protein	O
is	O
shown	O
adopting	O
different	O
shapes	O
(	O
conformations	O
)	O
in	O
its	O
search	O
for	O
the	O
lowest	O
energy	O
structure	O
.	O
</s>
<s>
Three	O
graphs	O
are	O
included	O
in	O
the	O
screensaver	B-General_Concept
.	O
</s>
<s>
A	O
graph	O
of	O
the	O
accepted	O
model	O
's	O
root-mean-square	B-General_Concept
deviation	I-General_Concept
(	O
RMSD	B-General_Concept
)	O
,	O
which	O
measures	O
how	O
structurally	O
similar	O
the	O
accepted	O
model	O
is	O
to	O
the	O
native	O
model	O
,	O
is	O
shown	O
far	O
right	O
.	O
</s>
<s>
On	O
the	O
right	O
of	O
the	O
accepted	O
energy	O
graph	O
and	O
below	O
the	O
RMSD	B-General_Concept
graph	O
,	O
the	O
results	O
from	O
these	O
two	O
functions	O
are	O
used	O
to	O
produce	O
an	O
energy	O
vs.	O
RMSD	B-General_Concept
plot	O
as	O
the	O
model	O
is	O
progressively	O
refined	O
.	O
</s>
<s>
Like	O
all	O
BOINC	B-Operating_System
projects	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
runs	O
in	O
the	O
background	O
of	O
the	O
user	O
's	O
computer	O
,	O
using	O
idle	O
computer	O
power	O
,	O
either	O
at	O
or	O
before	O
logging	O
into	O
an	O
account	O
on	O
the	O
host	O
operating	B-General_Concept
system	I-General_Concept
.	O
</s>
<s>
Rosetta	O
,	O
the	O
software	O
that	O
runs	O
on	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
network	O
,	O
was	O
rewritten	O
in	O
C++	B-Language
to	O
allow	O
easier	O
development	O
than	O
that	O
allowed	O
by	O
its	O
original	O
version	O
,	O
which	O
was	O
written	O
in	O
Fortran	B-Application
.	O
</s>
<s>
This	O
new	O
version	O
is	O
object-oriented	B-Language
,	O
and	O
was	O
released	O
on	O
February	O
8	O
,	O
2008	O
.	O
</s>
<s>
Protein	O
3D	O
structures	O
are	O
currently	O
determined	O
experimentally	O
via	O
X-ray	B-Library
crystallography	O
or	O
nuclear	O
magnetic	O
resonance	O
(	O
NMR	O
)	O
spectroscopy	O
.	O
</s>
<s>
One	O
of	O
the	O
main	O
goals	O
of	O
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
to	O
predict	O
protein	O
structures	O
with	O
the	O
same	O
accuracy	O
as	O
existing	O
methods	O
,	O
but	O
in	O
a	O
way	O
that	O
requires	O
significantly	O
less	O
time	O
and	O
money	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
also	O
develops	O
methods	O
to	O
determine	O
the	O
structure	O
and	O
docking	O
of	O
membrane	O
proteins	O
(	O
e.g.	O
,	O
G	O
protein	O
–	O
coupled	O
receptors	O
(	O
GPCRs	O
)	O
)	O
,	O
which	O
are	O
exceptionally	O
difficult	O
to	O
analyze	O
with	O
traditional	O
techniques	O
like	O
X-ray	B-Library
crystallography	O
and	O
NMR	O
spectroscopy	O
,	O
yet	O
represent	O
the	O
majority	O
of	O
targets	O
for	O
modern	O
drugs	O
.	O
</s>
<s>
Rosetta	O
,	O
the	O
program	O
on	O
which	O
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
based	O
,	O
has	O
been	O
used	O
since	O
CASP5	O
in	O
2002	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
has	O
been	O
used	O
in	O
CASP	O
since	O
2006	O
,	O
where	O
it	O
was	O
among	O
the	O
top	O
predictors	O
in	O
every	O
category	O
of	O
structure	O
prediction	O
in	O
CASP7	O
.	O
</s>
<s>
These	O
high	O
quality	O
predictions	O
were	O
enabled	O
by	O
the	O
computing	O
power	O
made	O
available	O
by	O
Rosetta	B-Operating_System
@home	I-Operating_System
volunteers	O
.	O
</s>
<s>
Increasing	O
computing	O
power	O
allows	O
Rosetta	B-Operating_System
@home	I-Operating_System
to	O
sample	O
more	O
regions	O
of	O
conformation	O
space	O
(	O
the	O
possible	O
shapes	O
a	O
protein	O
can	O
assume	O
)	O
,	O
which	O
,	O
according	O
to	O
Levinthal	O
's	O
paradox	O
,	O
is	O
predicted	O
to	O
increase	O
exponentially	O
with	O
protein	O
length	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
also	O
used	O
in	O
protein	O
–	O
protein	O
docking	O
prediction	O
,	O
which	O
determines	O
the	O
structure	O
of	O
multiple	O
complexed	O
proteins	O
,	O
or	O
quaternary	O
structure	O
.	O
</s>
<s>
Rosetta	O
is	O
used	O
in	O
the	O
Critical	O
Assessment	O
of	O
Prediction	O
of	O
Interactions	O
(	O
CAPRI	B-Application
)	O
experiment	O
,	O
which	O
evaluates	O
the	O
state	O
of	O
the	O
protein	O
docking	O
field	O
similar	O
to	O
how	O
CASP	O
gauges	O
progress	O
in	O
protein	O
structure	O
prediction	O
.	O
</s>
<s>
The	O
computing	O
power	O
made	O
available	O
by	O
home	O
's	O
project	O
volunteers	O
has	O
been	O
cited	O
as	O
a	O
major	O
factor	O
in	O
Rosetta	O
's	O
performance	O
in	O
CAPRI	B-Application
,	O
where	O
its	O
docking	O
predictions	O
have	O
been	O
among	O
the	O
most	O
accurate	O
and	O
complete	O
.	O
</s>
<s>
The	O
2008	O
research	O
paper	O
from	O
David	O
Baker	O
's	O
group	O
describing	O
how	O
the	O
protein	O
was	O
made	O
,	O
which	O
cited	O
Rosetta	B-Operating_System
@home	I-Operating_System
for	O
the	O
computing	O
resources	O
it	O
made	O
available	O
,	O
represented	O
an	O
important	O
proof	O
of	O
concept	O
for	O
this	O
protein	O
design	O
method	O
.	O
</s>
<s>
In	O
addition	O
to	O
basic	O
research	O
in	O
predicting	O
protein	O
structure	O
,	O
docking	O
and	O
design	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
also	O
used	O
in	O
immediate	O
disease-related	O
research	O
.	O
</s>
<s>
Numerous	O
minor	O
research	O
projects	O
are	O
described	O
in	O
David	O
Baker	O
's	O
Rosetta	B-Operating_System
@home	I-Operating_System
journal	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
was	O
used	O
in	O
the	O
same	O
study	O
to	O
predict	O
structures	O
for	O
amyloid	O
beta	O
,	O
a	O
fibril-forming	O
protein	O
that	O
has	O
been	O
postulated	O
to	O
cause	O
Alzheimer	O
's	O
disease	O
.	O
</s>
<s>
The	O
protein	O
complex	O
predicted	O
by	O
RosettaDock	O
closely	O
agreed	O
with	O
the	O
especially	O
difficult-to-obtain	O
experimental	O
models	B-Application
,	O
leading	O
researchers	O
to	O
conclude	O
that	O
the	O
docking	O
method	O
has	O
potential	O
to	O
address	O
some	O
of	O
the	O
problems	O
that	O
X-ray	B-Library
crystallography	O
has	O
with	O
modelling	O
protein	O
–	O
protein	O
interfaces	O
.	O
</s>
<s>
As	O
part	O
of	O
research	O
funded	O
by	O
a	O
$19.4	O
million	O
grant	O
by	O
the	O
Bill	O
&	O
Melinda	O
Gates	O
Foundation	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
has	O
been	O
used	O
in	O
designing	O
multiple	O
possible	O
vaccines	O
for	O
human	O
immunodeficiency	O
virus	O
(	O
HIV	O
)	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
was	O
used	O
to	O
help	O
screen	O
the	O
over	O
2	O
million	O
SARS-CoV-2	O
Spike-binding	O
proteins	O
that	O
were	O
computationally	O
designed	O
,	O
and	O
thus	O
,	O
contributed	O
to	O
this	O
research	O
.	O
</s>
<s>
Per	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
team	O
at	O
the	O
Institute	O
of	O
Protein	O
Design	O
,	O
Rosetta	B-Operating_System
@home	I-Operating_System
volunteers	O
contributed	O
to	O
the	O
development	O
of	O
antiviral	O
drug	O
candidates	O
and	O
to	O
a	O
protein	O
nanoparticle	O
vaccine	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
researchers	O
have	O
designed	O
an	O
IL-2	O
receptor	O
agonist	O
called	O
Neoleukin-2/15	O
that	O
does	O
not	O
interact	O
with	O
the	O
alpha	O
subunit	O
of	O
the	O
receptor	O
.	O
</s>
<s>
While	O
the	O
natural	O
IL-2	O
suffers	O
from	O
toxicity	O
due	O
to	O
an	O
interaction	O
with	O
the	O
alpha	O
subunit	O
,	O
the	O
designed	O
protein	O
is	O
much	O
safer	O
,	O
at	O
least	O
in	O
animal	O
models	B-Application
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
contributed	O
in	O
"	O
forward	O
folding	O
experiments	O
"	O
which	O
helped	O
validate	O
designs	O
.	O
</s>
<s>
The	O
Rosetta	O
platform	O
derives	O
its	O
name	O
from	O
the	O
Rosetta	B-Operating_System
Stone	I-Operating_System
,	O
as	O
it	O
attempts	O
to	O
decipher	O
the	O
structural	O
"	O
meaning	O
"	O
of	O
proteins	O
 '	O
amino	O
acid	O
sequences	O
.	O
</s>
<s>
More	O
than	O
sevenyears	O
after	O
Rosetta	O
's	O
first	O
appearance	O
,	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
project	O
was	O
released	O
(	O
i.e.	O
,	O
announced	O
as	O
no	O
longer	O
beta	O
)	O
on	O
October	O
6	O
,	O
2005	O
.	O
</s>
<s>
This	O
new	O
conformation	O
was	O
predicted	O
by	O
Rosetta	O
to	O
within	O
1.2Å	O
RMSD	B-General_Concept
of	O
the	O
structure	O
determined	O
by	O
X-ray	B-Library
crystallography	O
,	O
representing	O
an	O
unusually	O
accurate	O
structure	O
prediction	O
.	O
</s>
<s>
The	O
visible	O
product	O
of	O
that	O
research	O
,	O
Top7	O
,	O
was	O
featured	O
as	O
the	O
RCSB	O
PDB	O
's	O
'	O
Molecule	O
of	O
the	O
Month	O
 '	O
in	O
October	O
2006	O
;	O
a	O
superposition	O
of	O
the	O
respective	O
cores	O
(	O
residues	O
60	O
–	O
79	O
)	O
of	O
its	O
predicted	O
and	O
X-ray	B-Library
crystal	O
structures	O
are	O
featured	O
in	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
logo	O
.	O
</s>
<s>
RosettaDock	O
was	O
added	O
to	O
the	O
Rosetta	O
software	O
suite	O
during	O
the	O
first	O
CAPRI	B-Application
experiment	O
in	O
2002	O
as	O
the	O
Baker	O
laboratory	O
's	O
algorithm	O
for	O
protein	O
–	O
protein	O
docking	O
prediction	O
.	O
</s>
<s>
While	O
the	O
RosettaDock	O
method	O
only	O
made	O
two	O
acceptably	O
accurate	O
predictions	O
out	O
of	O
seven	O
possible	O
,	O
this	O
was	O
enough	O
to	O
rank	O
it	O
seventh	O
out	O
of	O
nineteen	O
prediction	O
methods	O
in	O
the	O
first	O
CAPRI	B-Application
assessment	O
.	O
</s>
<s>
Development	O
of	O
RosettaDock	O
diverged	O
into	O
two	O
branches	O
for	O
subsequent	O
CAPRI	B-Application
rounds	O
as	O
Jeffrey	O
Gray	O
,	O
who	O
laid	O
the	O
groundwork	O
for	O
RosettaDock	O
while	O
at	O
the	O
University	O
of	O
Washington	O
,	O
continued	O
working	O
on	O
the	O
method	O
in	O
his	O
new	O
position	O
at	O
Johns	O
Hopkins	O
University	O
.	O
</s>
<s>
Despite	O
these	O
differences	O
,	O
both	O
the	O
Baker	O
and	O
Gray	O
methods	O
performed	O
well	O
in	O
the	O
second	O
CAPRI	B-Application
assessment	O
,	O
placing	O
fifth	O
and	O
seventh	O
respectively	O
out	O
of	O
30	O
predictor	O
groups	O
.	O
</s>
<s>
Jeffrey	O
Gray	O
's	O
RosettaDock	O
server	B-Application
is	O
available	O
as	O
a	O
free	O
docking	O
prediction	O
service	O
for	O
non-commercial	O
use	O
.	O
</s>
<s>
In	O
October	O
2006	O
,	O
RosettaDock	O
was	O
integrated	O
into	O
Rosetta	B-Operating_System
@home	I-Operating_System
.	O
</s>
<s>
The	O
vastly	O
increased	O
computing	O
power	O
afforded	O
by	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
network	O
,	O
combined	O
with	O
revised	O
fold-tree	O
representations	O
for	O
backbone	O
flexibility	O
and	O
loop	O
modeling	O
,	O
made	O
RosettaDock	O
sixth	O
out	O
of	O
63	O
prediction	O
groups	O
in	O
the	O
third	O
CAPRI	B-Application
assessment	O
.	O
</s>
<s>
The	O
Robetta	O
(	O
Rosetta	O
Beta	O
)	O
server	B-Application
is	O
an	O
automated	O
protein	O
structure	O
prediction	O
service	O
offered	O
by	O
the	O
Baker	O
laboratory	O
for	O
non-commercial	O
ab	O
initio	O
and	O
comparative	O
modeling	O
.	O
</s>
<s>
It	O
has	O
participated	O
as	O
an	O
automated	O
prediction	O
server	B-Application
in	O
the	O
biannual	O
CASP	O
experiments	O
since	O
CASP5	O
in	O
2002	O
,	O
performing	O
among	O
the	O
best	O
in	O
the	O
automated	O
server	B-Application
prediction	O
category	O
.	O
</s>
<s>
Robetta	O
has	O
since	O
competed	O
in	O
CASP6	O
and	O
7	O
,	O
where	O
it	O
did	O
better	O
than	O
average	O
among	O
both	O
automated	O
server	B-Application
and	O
human	O
predictor	O
groups	O
.	O
</s>
<s>
In	O
modeling	O
protein	O
structure	O
as	O
of	O
CASP6	O
,	O
Robetta	O
first	O
searches	O
for	O
structural	O
homologs	O
using	O
BLAST	B-Application
,	O
PSI-BLAST	O
,	O
and	O
3D-Jury	O
,	O
then	O
parses	O
the	O
target	O
sequence	O
into	O
its	O
individual	O
domains	O
,	O
or	O
independently	O
folding	O
units	O
of	O
proteins	O
,	O
by	O
matching	O
the	O
sequence	O
to	O
structural	O
families	O
in	O
the	O
Pfam	O
database	O
.	O
</s>
<s>
Finally	O
,	O
side-chain	O
contributions	O
are	O
modeled	O
using	O
a	O
protocol	O
for	O
Monte	B-Algorithm
Carlo	I-Algorithm
conformational	O
search	O
.	O
</s>
<s>
In	O
CASP8	O
,	O
Robetta	O
was	O
augmented	O
to	O
use	O
Rosetta	O
's	O
high	O
resolution	O
all-atom	O
refinement	O
method	O
,	O
the	O
absence	O
of	O
which	O
was	O
cited	O
as	O
the	O
main	O
cause	O
for	O
Robetta	O
being	O
less	O
accurate	O
than	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
network	O
in	O
CASP7	O
.	O
</s>
<s>
On	O
May	O
9	O
,	O
2008	O
,	O
after	O
Rosetta	B-Operating_System
@home	I-Operating_System
users	O
suggested	O
an	O
interactive	O
version	O
of	O
the	O
volunteer	B-Operating_System
computing	I-Operating_System
program	O
,	O
the	O
Baker	O
lab	O
publicly	O
released	O
Foldit	B-Language
,	O
an	O
online	O
protein	O
structure	O
prediction	O
game	O
based	O
on	O
the	O
Rosetta	O
platform	O
.	O
</s>
<s>
,	O
Foldit	B-Language
had	O
over	O
59,000	O
registered	O
users	O
.	O
</s>
<s>
There	O
are	O
several	O
volunteer	O
computed	O
projects	O
which	O
have	O
study	O
areas	O
similar	O
to	O
those	O
of	O
Rosetta	B-Operating_System
@home	I-Operating_System
,	O
but	O
differ	O
in	O
their	O
research	O
approach	O
:	O
</s>
<s>
Of	O
all	O
the	O
major	O
volunteer	B-Operating_System
computing	I-Operating_System
projects	O
involved	O
in	O
protein	O
research	O
,	O
Folding	B-Application
@home	I-Application
is	O
the	O
only	O
one	O
not	O
using	O
the	O
BOINC	B-Operating_System
platform	O
.	O
</s>
<s>
Both	O
Rosetta	B-Operating_System
@home	I-Operating_System
and	O
Folding	B-Application
@home	I-Application
study	O
protein	O
misfolding	O
diseases	O
such	O
as	O
Alzheimer	O
's	O
disease	O
,	O
but	O
Folding	B-Application
@home	I-Application
does	O
so	O
much	O
more	O
exclusively	O
.	O
</s>
<s>
Folding	B-Application
@home	I-Application
almost	O
exclusively	O
uses	O
all-atom	O
molecular	O
dynamics	O
models	B-Application
to	O
understand	O
how	O
and	O
why	O
proteins	O
fold	O
(	O
or	O
potentially	O
misfold	O
,	O
and	O
subsequently	O
aggregate	O
to	O
cause	O
diseases	O
)	O
.	O
</s>
<s>
Some	O
of	O
home	O
's	O
results	O
are	O
used	O
as	O
the	O
basis	O
for	O
some	O
Folding	B-Application
@home	I-Application
projects	O
.	O
</s>
<s>
Folding	B-Application
@home	I-Application
can	O
then	O
be	O
used	O
to	O
verify	O
home	O
's	O
results	O
,	O
and	O
can	O
provide	O
added	O
atomic-level	O
information	O
,	O
and	O
details	O
of	O
how	O
the	O
molecule	O
changes	O
shape	O
.	O
</s>
<s>
Averaging	O
about	O
6,650	O
teraFLOPS	O
from	O
a	O
host	O
base	O
of	O
central	B-General_Concept
processing	I-General_Concept
units	I-General_Concept
(	O
CPUs	O
)	O
,	O
graphics	B-Architecture
processing	I-Architecture
units	I-Architecture
(	O
GPUs	B-Architecture
)	O
,	O
and	O
(	O
formerly	O
)	O
PS3s	B-Operating_System
,	O
Folding	B-Application
@home	I-Application
has	O
nearly	O
108	O
times	O
more	O
computing	O
power	O
than	O
Rosetta	B-Operating_System
@home	I-Operating_System
.	O
</s>
<s>
Both	O
Phase	O
I	O
and	O
Phase	O
II	O
of	O
the	O
Human	B-Operating_System
Proteome	I-Operating_System
Folding	I-Operating_System
Project	I-Operating_System
(	O
HPF	O
)	O
,	O
a	O
subproject	O
of	O
World	B-Operating_System
Community	I-Operating_System
Grid	I-Operating_System
,	O
have	O
used	O
the	O
Rosetta	O
program	O
to	O
make	O
structural	O
and	O
functional	O
annotations	O
of	O
various	O
genomes	O
.	O
</s>
<s>
Although	O
he	O
now	O
uses	O
it	O
to	O
create	O
databases	O
for	O
biologists	O
,	O
Richard	O
Bonneau	O
,	O
head	O
scientist	O
of	O
the	O
Human	B-Operating_System
Proteome	I-Operating_System
Folding	I-Operating_System
Project	I-Operating_System
,	O
was	O
active	O
in	O
the	O
original	O
development	O
of	O
Rosetta	O
at	O
David	O
Baker	O
's	O
laboratory	O
while	O
obtaining	O
his	O
PhD	O
.	O
</s>
<s>
More	O
information	O
on	O
the	O
relationship	O
between	O
the	O
HPF1	O
,	O
HPF2	O
and	O
Rosetta	B-Operating_System
@home	I-Operating_System
can	O
be	O
found	O
on	O
Richard	O
Bonneau	O
's	O
website	O
.	O
</s>
<s>
Like	O
Rosetta	B-Operating_System
@home	I-Operating_System
,	O
Predictor	B-Operating_System
@home	I-Operating_System
specialized	O
in	O
protein	O
structure	O
prediction	O
.	O
</s>
<s>
While	O
Rosetta	B-Operating_System
@home	I-Operating_System
uses	O
the	O
Rosetta	O
program	O
for	O
its	O
structure	O
prediction	O
,	O
Predictor	B-Operating_System
@home	I-Operating_System
used	O
the	O
dTASSER	O
methodology	O
.	O
</s>
<s>
In	O
2009	O
,	O
Predictor	B-Operating_System
@home	I-Operating_System
shut	O
down	O
.	O
</s>
<s>
Other	O
protein	O
related	O
volunteer	B-Operating_System
computing	I-Operating_System
projects	O
on	O
BOINC	B-Operating_System
include	O
QMC	B-Operating_System
@home	I-Operating_System
,	O
Docking	B-Operating_System
@home	I-Operating_System
,	O
POEM	B-Operating_System
@home	I-Operating_System
,	O
SIMAP	B-Operating_System
,	O
and	O
TANPAKU	O
.	O
</s>
<s>
RALPH	B-Operating_System
@home	I-Operating_System
,	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
alpha	O
project	O
which	O
tests	O
new	O
application	O
versions	O
,	O
work	O
units	O
,	O
and	O
updates	O
before	O
they	O
move	O
on	O
to	O
Rosetta	B-Operating_System
@home	I-Operating_System
,	O
runs	O
on	O
BOINC	B-Operating_System
also	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
depends	O
on	O
computing	O
power	O
donated	O
by	O
individual	O
project	O
members	O
for	O
its	O
research	O
.	O
</s>
<s>
,	O
about	O
53,000	O
users	O
from	O
150	O
countries	O
were	O
active	O
members	O
of	O
Rosetta	B-Operating_System
@home	I-Operating_System
,	O
together	O
contributing	O
idle	O
processor	O
time	O
from	O
about	O
54,800	O
computers	O
for	O
a	O
combined	O
average	O
performance	O
of	O
over	O
1.7	O
PetaFLOPS	O
.	O
</s>
<s>
Users	O
are	O
granted	O
BOINC	B-Operating_System
credits	I-Operating_System
as	O
a	O
measure	O
of	O
their	O
contribution	O
.	O
</s>
<s>
The	O
credit	O
granted	O
for	O
each	O
workunit	B-Operating_System
is	O
the	O
number	O
of	O
decoys	O
produced	O
for	O
that	O
workunit	B-Operating_System
multiplied	O
by	O
the	O
average	O
claimed	O
credit	O
for	O
the	O
decoys	O
submitted	O
by	O
all	O
computer	O
hosts	O
for	O
that	O
workunit	B-Operating_System
.	O
</s>
<s>
This	O
custom	O
system	O
was	O
designed	O
to	O
address	O
significant	O
differences	O
between	O
credit	O
granted	O
to	O
users	O
with	O
the	O
standard	O
BOINC	B-Operating_System
client	O
and	O
an	O
optimized	O
BOINC	B-Operating_System
client	O
,	O
and	O
credit	O
differences	O
between	O
users	O
running	O
Rosetta	B-Operating_System
@home	I-Operating_System
on	O
Windows	B-Application
and	O
Linux	B-Application
operating	I-Application
systems	I-Application
.	O
</s>
<s>
The	O
amount	O
of	O
credit	O
granted	O
per	O
second	O
of	O
CPU	O
work	O
is	O
lower	O
for	O
Rosetta	B-Operating_System
@home	I-Operating_System
than	O
most	O
other	O
BOINC	B-Operating_System
projects	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
is	O
thirteenth	O
out	O
of	O
over	O
40	O
BOINC	B-Operating_System
projects	O
in	O
terms	O
of	O
total	O
credit	O
.	O
</s>
<s>
Rosetta	B-Operating_System
@home	I-Operating_System
users	O
who	O
predict	O
protein	O
structures	O
submitted	O
for	O
the	O
CASP	O
experiment	O
are	O
acknowledged	O
in	O
scientific	O
publications	O
regarding	O
their	O
results	O
.	O
</s>
<s>
Users	O
who	O
predict	O
the	O
lowest	O
energy	O
structure	O
for	O
a	O
given	O
workunit	B-Operating_System
are	O
featured	O
on	O
the	O
Rosetta	B-Operating_System
@home	I-Operating_System
homepage	O
as	O
Predictor	O
of	O
the	O
Day	O
,	O
along	O
with	O
any	O
team	O
of	O
which	O
they	O
are	O
a	O
member	O
.	O
</s>
<s>
A	O
User	O
of	O
the	O
Day	O
is	O
chosen	O
randomly	O
each	O
day	O
to	O
be	O
on	O
the	O
homepage	O
also	O
,	O
from	O
among	O
users	O
who	O
have	O
made	O
a	O
Rosetta	B-Operating_System
@home	I-Operating_System
profile	O
.	O
</s>
