<s>
The	O
Re-referenced	O
Protein	O
Chemical	O
shift	O
Database	O
(	O
RefDB	B-Application
)	O
is	O
an	O
NMR	O
spectroscopy	O
database	O
of	O
carefully	O
corrected	O
or	O
re-referenced	O
chemical	O
shifts	O
,	O
derived	O
from	O
the	O
BioMagResBank	O
(	O
BMRB	O
)	O
(	O
Fig	O
.	O
</s>
<s>
The	O
database	O
was	O
assembled	O
by	O
using	O
a	O
structure-based	O
chemical	O
shift	O
calculation	O
program	O
(	O
called	O
SHIFTX	O
)	O
to	O
calculate	O
expected	O
protein	O
(	O
1	O
)	O
H	O
,	O
(	O
13	O
)	O
C	O
and	O
(	O
15	O
)	O
N	O
chemical	O
shifts	O
from	O
X-ray	B-Library
or	O
NMR	O
coordinate	O
data	O
of	O
previously	O
assigned	O
proteins	O
reported	O
in	O
the	O
BMRB	O
.	O
</s>
<s>
The	O
comparison	O
is	O
automatically	O
performed	O
by	O
a	O
program	O
called	O
SHIFTCOR	B-Application
.	O
</s>
<s>
The	O
RefDB	B-Application
database	O
currently	O
provides	O
reference-corrected	O
chemical	O
shift	O
data	O
on	O
more	O
than	O
2000	O
assigned	O
peptides	O
and	O
proteins	O
.	O
</s>
<s>
Users	O
may	O
download	O
,	O
search	O
or	O
browse	O
the	O
database	O
through	O
a	O
number	O
of	O
methods	O
available	O
through	O
the	O
RefDB	B-Application
website	O
.	O
</s>
<s>
RefDB	B-Application
provides	O
a	O
standard	O
chemical	O
shift	O
resource	O
for	O
biomolecular	O
NMR	O
spectroscopists	O
,	O
wishing	O
to	O
derive	O
or	O
compute	O
chemical	O
shift	O
trends	O
in	O
peptides	O
and	O
proteins	O
.	O
</s>
<s>
All	O
data	O
in	O
RefDB	B-Application
is	O
non-proprietary	O
or	O
is	O
derived	O
from	O
a	O
non-proprietary	O
source	O
.	O
</s>
<s>
RefDB	B-Application
data	O
is	O
available	O
through	O
a	O
public	O
web	O
interface	O
and	O
downloads	O
.	O
</s>
<s>
All	O
chemical	O
shifts	O
in	O
RefDB	B-Application
have	O
been	O
computationally	O
re-referenced	O
to	O
DSS	O
(	O
a	O
common	O
NMR	O
chemical	O
shift	O
standard	O
)	O
.	O
</s>
<s>
RefDB	B-Application
is	O
a	O
continuously	O
updated	O
resource	O
that	O
uses	O
web-bots	O
to	O
query	O
public	O
databases	O
(	O
BMRB	O
,	O
GenBank	O
,	O
Protein	O
Data	O
Bank	O
)	O
and	O
fetch	O
assignment	O
,	O
sequence	O
and	O
structure	O
data	O
on	O
a	O
weekly	O
basis	O
.	O
</s>
<s>
RefDB	B-Application
is	O
fully	O
web-enabled	O
database	O
,	O
it	O
stores	O
data	O
in	O
two	O
standard	O
formats	O
(	O
NMR-STAR	O
and	O
Shifty	O
)	O
,	O
it	O
performs	O
automated	O
data	O
updating	O
,	O
checking	O
and	O
validation	O
and	O
it	O
provides	O
open	O
access	O
to	O
output	O
data	O
in	O
a	O
fully	O
downloadable	O
flat	O
file	O
format	O
as	O
well	O
as	O
in	O
a	O
hyperlinked	O
browsable	O
table	O
(	O
see	O
Fig	O
.	O
</s>
<s>
RefDB	B-Application
also	O
supports	O
keyword	O
queries	O
and	O
sequence	O
searches	O
(	O
using	O
local	O
BLAST	B-Application
)	O
.	O
</s>
<s>
RefDB	B-Application
is	O
usually	O
updated	O
on	O
a	O
weekly	O
basis	O
.	O
</s>
<s>
The	O
RefDB	B-Application
database	O
,	O
along	O
with	O
its	O
associated	O
software	O
,	O
is	O
freely	O
available	O
at	O
and	O
at	O
the	O
BMRB	O
website	O
.	O
</s>
<s>
RefDB	B-Application
has	O
been	O
prepared	O
using	O
a	O
combination	O
of	O
three	O
different	O
computer	O
programs	O
.	O
</s>
<s>
The	O
second	O
program	O
(	O
SHIFTCOR	B-Application
)	O
compares	O
the	O
calculated	O
shifts	O
with	O
the	O
observed	O
shifts	O
,	O
evaluates	O
any	O
statistically	O
significant	O
differences	O
and	O
performs	O
the	O
necessary	O
chemical	O
shift	O
corrections	O
.	O
</s>
<s>
UPDATE	O
also	O
directs	O
the	O
data	O
to	O
SHIFTCOR	B-Application
and	O
appends	O
the	O
‘	O
corrected’	O
chemical	O
shift	O
file	O
to	O
the	O
RefDB	B-Application
database	O
.	O
</s>
