<s>
RAPTOR	B-Application
is	O
protein	O
threading	O
software	O
used	O
for	O
protein	O
structure	O
prediction	O
.	O
</s>
<s>
It	O
has	O
been	O
replaced	O
by	O
RaptorX	B-Application
,	O
which	O
is	O
much	O
more	O
accurate	O
than	O
RAPTOR	B-Application
.	O
</s>
<s>
Initial	O
steps	O
may	O
include	O
performing	O
a	O
PSI-BLAST	O
or	O
PatternHunter	B-Application
search	O
to	O
locate	O
a	O
similar	O
sequences	O
with	O
a	O
known	O
structure	O
in	O
the	O
Protein	O
Data	O
Bank	O
(	O
PDB	O
)	O
.	O
</s>
<s>
Where	O
these	O
techniques	O
are	O
too	O
expensive	O
,	O
time-consuming	O
or	O
limited	O
in	O
scope	O
,	O
researchers	O
can	O
use	O
protein	O
threading	O
software	O
,	O
such	O
as	O
RAPTOR	B-Application
to	O
create	O
a	O
highly	O
reliable	O
model	O
of	O
the	O
protein	O
.	O
</s>
<s>
Protein	O
threading	O
is	O
more	O
effective	O
than	O
homology	O
modeling	O
,	O
especially	O
for	O
proteins	O
which	O
have	O
few	O
homologs	O
detectable	O
by	O
sequence	B-Algorithm
alignment	I-Algorithm
.	O
</s>
<s>
Unlike	O
homology	O
modeling	O
,	O
which	O
selects	O
template	O
purely	O
based	O
on	O
homology	O
information	O
(	O
sequence	B-Algorithm
alignments	I-Algorithm
)	O
,	O
the	O
scoring	O
function	O
used	O
in	O
protein	O
threading	O
utilizes	O
both	O
homology	O
and	O
structure	O
information	O
(	O
sequence	O
structure	O
alignments	O
)	O
.	O
</s>
<s>
Failed	O
attempts	O
to	O
obtain	O
a	O
good	O
template	O
with	O
BLAST	O
often	O
result	O
in	O
users	O
processing	O
results	O
through	O
RAPTOR	B-Application
.	O
</s>
<s>
The	O
integer	B-Algorithm
programming	I-Algorithm
approach	O
to	O
RAPTOR	B-Application
produces	O
higher	O
quality	O
models	O
than	O
other	O
protein	O
threading	O
methods	O
.	O
</s>
<s>
Most	O
threading	O
software	O
use	O
dynamic	B-Algorithm
programming	I-Algorithm
to	O
optimize	O
their	O
scoring	O
functions	O
when	O
aligning	O
a	O
sequence	O
with	O
a	O
template	O
.	O
</s>
<s>
Dynamic	B-Algorithm
programming	I-Algorithm
is	O
much	O
easier	O
to	O
implement	O
than	O
integer	B-Algorithm
programming	I-Algorithm
;	O
however	O
if	O
a	O
scoring	O
function	O
has	O
pairwise	O
contact	O
potential	O
included	O
,	O
dynamic	B-Algorithm
programming	I-Algorithm
cannot	O
globally	O
optimize	O
such	O
a	O
scoring	O
function	O
and	O
instead	O
just	O
generates	O
a	O
local	O
optimal	O
alignment	O
.	O
</s>
<s>
Integer	B-Algorithm
programming	I-Algorithm
can	O
globally	O
optimize	O
a	O
scoring	O
function	O
with	O
pairwise	O
contact	O
potential	O
and	O
produce	O
a	O
global	O
optimal	O
alignment	O
.	O
</s>
<s>
NoCore	O
,	O
NPCore	O
and	O
IP	O
are	O
the	O
three	O
different	O
threading	O
engines	O
implemented	O
in	O
RAPTOR	B-Application
.	O
</s>
<s>
NoCore	O
and	O
NPCore	O
are	O
based	O
on	O
dynamic	B-Algorithm
programming	I-Algorithm
and	O
faster	O
than	O
IP	O
.	O
</s>
<s>
IP	O
is	O
RAPTOR	B-Application
's	O
unique	O
integer	O
programming-based	O
threading	O
engine	O
.	O
</s>
<s>
The	O
default	O
3D	O
structure	O
modeling	O
tool	O
used	O
in	O
RAPTOR	B-Application
is	O
OWL	O
.	O
</s>
<s>
OWL	O
is	O
automatically	O
called	O
in	O
RAPTOR	B-Application
to	O
generate	O
the	O
3D	O
output	O
.	O
</s>
<s>
If	O
a	O
researcher	O
has	O
MODELLER	O
,	O
they	O
can	O
also	O
set	O
up	O
RAPTOR	B-Application
to	O
call	O
MODELLER	O
automatically	O
.	O
</s>
<s>
RAPTOR	B-Application
can	O
also	O
generate	O
ICM-Pro	O
input	O
files	O
,	O
with	O
which	O
people	O
run	O
ICM-Pro	O
by	O
themselves	O
.	O
</s>
<s>
To	O
make	O
it	O
a	O
comprehensive	O
tool	O
set	O
,	O
PSI-BLAST	O
is	O
also	O
included	O
in	O
RAPTOR	B-Application
to	O
let	O
people	O
do	O
homology	O
modeling	O
.	O
</s>
<s>
In	O
RAPTOR	B-Application
,	O
Jmol	B-Language
is	O
used	O
as	O
the	O
structure	O
viewer	O
for	O
examining	O
the	O
generated	O
prediction	O
.	O
</s>
<s>
For	O
each	O
template	O
,	O
people	O
can	O
view	O
the	O
alignment	O
,	O
E-value	B-General_Concept
and	O
numerous	O
other	O
specific	O
scores	O
.	O
</s>
<s>
RAPTOR	B-Application
first	O
appeared	O
in	O
CAFASP3	O
(	O
CASP5	O
)	O
in	O
2002	O
and	O
was	O
ranked	O
number	O
one	O
in	O
the	O
individual	O
server	O
group	O
for	O
that	O
year	O
.	O
</s>
<s>
Since	O
then	O
,	O
RAPTOR	B-Application
has	O
actively	O
participated	O
in	O
every	O
CASP	O
for	O
evaluation	O
purpose	O
and	O
been	O
consistently	O
ranked	O
in	O
the	O
top	O
tier	O
.	O
</s>
<s>
According	O
to	O
the	O
ranking	O
from	O
Zhang	O
's	O
group	O
,	O
RAPTOR	B-Application
ranked	O
2nd	O
among	O
all	O
the	O
servers	O
(	O
meta	O
server	O
and	O
individual	O
servers	O
)	O
.	O
</s>
