<s>
RaptorX	B-Application
is	O
a	O
software	O
and	O
web	O
server	O
for	O
protein	O
structure	O
and	O
function	O
prediction	O
that	O
is	O
free	O
for	O
non-commercial	O
use	O
.	O
</s>
<s>
RaptorX	B-Application
is	O
among	O
the	O
most	O
popular	O
methods	O
for	O
protein	O
structure	O
prediction	O
.	O
</s>
<s>
Like	O
other	O
remote	O
homology	O
recognition/protein	O
threading	O
techniques	O
,	O
RaptorX	B-Application
is	O
able	O
to	O
regularly	O
generate	O
reliable	O
protein	O
models	O
when	O
the	O
widely	O
used	O
PSI-BLAST	B-Application
cannot	O
.	O
</s>
<s>
However	O
,	O
RaptorX	B-Application
is	O
also	O
significantly	O
different	O
from	O
those	O
profile-based	O
methods	O
(	O
e.g.	O
,	O
HHPred	B-Application
and	O
Phyre2	B-Application
)	O
in	O
that	O
RaptorX	B-Application
excels	O
at	O
modeling	O
of	O
protein	O
sequences	O
without	O
a	O
large	O
number	O
of	O
sequence	O
homologs	O
by	O
exploiting	O
structure	O
information	O
.	O
</s>
<s>
RaptorX	B-Application
Server	O
has	O
been	O
designed	O
to	O
ensure	O
a	O
user-friendly	O
interface	O
for	O
users	O
inexpert	O
in	O
protein	O
structure	O
prediction	O
methods	O
.	O
</s>
<s>
The	O
RaptorX	B-Application
project	O
was	O
started	O
in	O
2008	O
and	O
RaptorX	B-Application
Server	O
was	O
released	O
to	O
the	O
public	O
in	O
2011	O
.	O
</s>
<s>
After	O
pasting	O
a	O
protein	O
sequence	O
into	O
the	O
RaptorX	B-Application
submission	O
form	O
,	O
a	O
user	O
will	O
typically	O
wait	O
a	O
couple	O
of	O
hours	O
(	O
depending	O
on	O
sequence	O
length	O
)	O
for	O
a	O
prediction	O
to	O
complete	O
.	O
</s>
<s>
RaptorX	B-Application
Server	O
currently	O
generates	O
the	O
following	O
results	O
:	O
3-state	O
and	O
8-state	O
secondary	O
structure	O
prediction	O
,	O
sequence-template	O
alignment	O
,	O
3D	O
structure	O
prediction	O
,	O
solvent	O
accessibility	O
prediction	O
,	O
disorder	O
prediction	O
and	O
binding	O
site	O
prediction	O
.	O
</s>
<s>
RaptorX	B-Application
Server	O
also	O
produces	O
some	O
confidence	O
scores	O
indicating	O
the	O
quality	O
of	O
the	O
predicted	O
3D	O
models	O
(	O
in	O
the	O
absence	O
of	O
their	O
corresponding	O
native	O
structures	O
)	O
.	O
</s>
<s>
For	O
example	O
,	O
it	O
produces	O
P-value	O
for	O
relative	O
global	O
quality	O
of	O
a	O
3D	O
model	O
,	O
GDT	O
(	O
Global	O
Distance	O
Test	O
)	O
and	O
uGDT	O
(	O
unnormalized-GDT	O
)	O
for	O
absolute	O
global	O
quality	O
of	O
a	O
3D	O
model	O
and	O
per-position	O
RMSD	B-General_Concept
for	O
absolute	O
local	O
quality	O
at	O
each	O
residue	O
of	O
a	O
3D	O
model	O
.	O
</s>
<s>
Applications	O
of	O
RaptorX	B-Application
include	O
protein	O
structure	O
prediction	O
,	O
function	O
prediction	O
,	O
protein	O
sequence-structure	O
alignment	O
,	O
evolutionary	O
classification	O
of	O
proteins	O
,	O
guiding	O
site-directed	O
mutagenesis	O
and	O
solving	O
protein	O
crystal	O
structures	O
by	O
molecular	O
replacement	O
.	O
</s>
<s>
In	O
the	O
CASP9	O
blind	O
protein	O
structure	O
prediction	O
experiment	O
,	O
RaptorX	B-Application
was	O
ranked	O
2nd	O
out	O
of	O
about	O
80	O
automatic	O
structure	O
prediction	O
servers	O
.	O
</s>
<s>
RaptorX	B-Application
also	O
generated	O
the	O
best	O
alignments	O
for	O
the	O
50	O
hardest	O
CASP9	O
TBM(template-based modeling )	O
targets	O
.	O
</s>
<s>
in	O
CASP10	O
,	O
RaptorX	B-Application
is	O
the	O
only	O
server	O
group	O
among	O
the	O
top	O
10	O
human/server	O
groups	O
for	O
the	O
15	O
most	O
difficult	O
CASP10	O
TBM	O
targets	O
.	O
</s>
<s>
RaptorX	B-Application
is	O
the	O
successor	O
to	O
the	O
RAPTOR	O
protein	O
structure	O
prediction	O
system	O
.	O
</s>
<s>
RaptorX	B-Application
was	O
designed	O
and	O
developed	O
by	O
a	O
research	O
group	O
led	O
by	O
Prof	O
.	O
Jinbo	O
Xu	O
at	O
the	O
Toyota	O
Technological	O
Institute	O
at	O
Chicago	O
.	O
</s>
