<s>
This	O
list	B-Application
of	I-Application
protein	I-Application
structure	I-Application
prediction	I-Application
software	I-Application
summarizes	O
notable	O
used	O
software	O
tools	O
in	O
protein	O
structure	O
prediction	O
,	O
including	O
homology	O
modeling	O
,	O
protein	O
threading	O
,	O
ab	O
initio	O
methods	O
,	O
secondary	O
structure	O
prediction	O
,	O
and	O
transmembrane	O
helix	O
and	O
signal	O
peptide	O
prediction	O
.	O
</s>
<s>
Name	O
Method	O
Description	O
Release	O
dateIntFOLDA	O
unified	O
interface	O
for	O
:	O
Tertiary	O
structure	O
prediction/3D	O
modelling	O
,	O
3D	O
model	O
quality	O
assessment	O
,	O
Intrinsic	O
disorder	O
prediction	O
,	O
Domain	O
prediction	O
,	O
Prediction	O
of	O
protein-ligand	O
binding	O
residuesAutomated	O
webserver	O
and	O
some	O
downloadable	O
programs	O
RaptorX	B-Application
remote	O
homology	O
detection	O
,	O
protein	O
3D	O
modeling	O
,	O
binding	O
site	O
prediction	O
Automated	O
webserver	O
and	O
Downloadable	O
program	O
Biskit	B-Application
wraps	O
external	O
programs	O
into	O
automated	O
workflow	O
BLAST	B-Application
search	O
,	O
T-Coffee	B-Application
alignment	O
,	O
and	O
MODELLER	B-Application
constructionESyPred3D	O
Template	O
detection	O
,	O
alignment	O
,	O
3D	O
modeling	O
Automated	O
webserver	O
FoldX	B-Application
Energy	O
calculations	O
and	O
protein	O
design	O
Downloadable	O
program	O
Phyre	B-Application
and	I-Application
Phyre2	I-Application
Remote	O
template	O
detection	O
,	O
alignment	O
,	O
3D	O
modeling	O
,	O
multi-templates	O
,	O
ab	O
initio	O
Webserver	O
with	O
job	O
manager	O
,	O
automatically	O
updated	O
fold	O
library	O
,	O
genome	O
searching	O
and	O
other	O
facilitiesHHpred	O
Template	O
detection	O
,	O
alignment	O
,	O
3D	O
modeling	O
Interactive	O
webserver	O
with	O
help	O
facility	O
MODELLER	B-Application
Satisfaction	O
of	O
spatial	O
restraints	O
Standalone	O
program	O
mainly	O
in	O
Fortran	B-Application
and	O
Python	B-Language
CONFOLD	O
Satisfaction	O
of	O
contact	O
and	O
distance	O
restraints	O
Standalone	O
program	O
mainly	O
in	O
Fortran	B-Application
and	O
Perl	B-Language
MOE	O
(	O
Molecular	B-Application
Operating	I-Application
Environment	I-Application
)	O
Template	O
identification	O
,	O
use	O
of	O
multiple	O
templates	O
and	O
accounting	O
for	O
other	O
environments	O
(	O
e.g.	O
</s>
<s>
Proprietary	O
platform	O
,	O
supported	O
on	O
Windows	O
,	O
Linux	O
and	O
Mac	O
ROBETTA	B-Operating_System
Rosetta	O
homology	O
modeling	O
and	O
ab	O
initio	O
fragment	O
assembly	O
with	O
Ginzu	O
domain	O
prediction	O
Webserver	O
BHAGEERATH-H	O
Combination	O
of	O
ab	O
initio	O
folding	O
and	O
homology	O
methods	O
Protein	O
tertiary	O
structure	O
predictions	O
SWISS-MODEL	B-Application
Local	O
similarity/fragment	O
assembly	O
Automated	O
webserver	O
(	O
based	O
on	O
ProModII	O
)	O
Yasara	B-Application
Detection	O
of	O
templates	O
,	O
alignment	O
,	O
modeling	O
incl	O
.	O
</s>
<s>
It	O
takes	O
about	O
one	O
hour	O
to	O
fold	O
proteins	O
with	O
~	O
300	O
AAs	O
ROBETTA	B-Operating_System
Rosetta	O
homology	O
modeling	O
and	O
ab	O
initio	O
fragment	O
assembly	O
with	O
Ginzu	O
domain	O
prediction	O
Webserver	O
Rosetta	B-Operating_System
@home	I-Operating_System
Distributed-computing	O
implementation	O
of	O
Rosetta	O
algorithm	O
Downloadable	O
program	O
Abalone	B-Application
Molecular	O
Dynamics	O
folding	O
ProgramC-QUARKC-QUARK	O
is	O
a	O
method	O
for	O
ab	O
initio	O
protein	O
structure	O
prediction	O
.	O
</s>
