<s>
Protein	B-Protocol
Structure	I-Protocol
Evaluation	I-Protocol
Suite	I-Protocol
&	I-Protocol
Server	I-Protocol
(	O
PROSESS	B-Protocol
)	O
is	O
a	O
freely	O
available	O
web	B-Application
server	I-Application
for	O
protein	O
structure	O
validation	O
.	O
</s>
<s>
PROSESS	B-Protocol
is	O
unique	O
among	O
structure	O
validation	O
servers	O
in	O
that	O
it	O
evaluates	O
both	O
coordinate	O
quality	O
and	O
experimental	O
data	O
quality	O
.	O
</s>
<s>
PROSESS	B-Protocol
is	O
also	O
able	O
to	O
use	O
NMR	O
chemical	O
shifts	O
(	O
as	O
well	O
as	O
NOEs	O
)	O
to	O
assess	O
or	O
validate	O
protein	O
structures	O
.	O
</s>
<s>
Specifically	O
,	O
PROSESS	B-Protocol
assesses	O
the	O
agreement	O
between	O
observed	O
chemical	O
shifts	O
and	O
ShiftX-predicted	O
HA	O
,	O
CA	O
,	O
CB	O
,	O
N	O
,	O
C	O
,	O
and	O
HN	O
NMR	O
chemical	O
shifts	O
.	O
</s>
<s>
In	O
addition	O
to	O
its	O
ability	O
to	O
validate	O
structures	O
using	O
chemical	O
shifts	O
,	O
PROSESS	B-Protocol
also	O
checks	O
many	O
other	O
protein	O
structure	O
parameters	O
including	O
covalent	O
bond	O
quality	O
,	O
non-covalent	O
bond	O
and	O
atomic	O
packing	O
quality	O
,	O
torsion	O
angle	O
quality	O
and	O
NOE	O
quality	O
(	O
i.e.	O
</s>
<s>
A	O
total	O
of	O
8	O
different	O
programs	O
(	O
see	O
PROSESS	B-Protocol
sub-programs	O
below	O
)	O
are	O
used	O
in	O
the	O
PROSESS	B-Protocol
evaluation	O
and	O
validation	O
process	O
.	O
</s>
<s>
PROSESS	B-Protocol
can	O
handle	O
single-chain	O
X-ray	O
models	O
,	O
multi-chain	O
X-ray	O
models	O
,	O
single-chain	O
NMR	O
ensembles	O
,	O
multi-chain	O
NMR	O
ensembles	O
of	O
monomeric	O
and	O
multimeric	O
proteins	O
.	O
</s>
<s>
In	O
addition	O
to	O
being	O
able	O
to	O
validate	O
NMR	O
protein	O
structures	O
,	O
PROSESS	B-Protocol
can	O
be	O
used	O
to	O
validate	O
or	O
evaluate	O
any	O
protein	O
model	O
,	O
regardless	O
of	O
how	O
it	O
was	O
solved	O
(	O
X-ray	O
,	O
NMR	O
,	O
comparative	O
modelling	O
,	O
etc	O
.	O
</s>
<s>
PROSESS	B-Protocol
generates	O
a	O
detailed	O
and	O
colorful	O
structure	O
validation	O
report	O
,	O
including	O
tables	O
,	O
color-coded	O
images	O
and	O
graphs	O
or	O
bar	O
charts	O
.	O
</s>
<s>
For	O
most	O
of	O
its	O
graphs	O
and	O
charts	O
,	O
PROSESS	B-Protocol
uses	O
a	O
simple	O
RAG	O
(	O
red	O
,	O
amber	O
,	O
green	O
)	O
color	O
scheme	O
to	O
indicate	O
the	O
quality	O
of	O
different	O
structure	O
parameters	O
for	O
the	O
protein	O
(	O
as	O
a	O
whole	O
)	O
,	O
for	O
different	O
members	O
of	O
the	O
structure	O
ensemble	O
,	O
for	O
specific	O
residues	O
and	O
for	O
specific	O
atoms	O
.	O
</s>
<s>
PROSESS	B-Protocol
's	O
quality	O
indices	O
and	O
quality	O
color	O
scales	O
have	O
been	O
designed	O
specifically	O
to	O
help	O
non-structural	O
biologists	O
to	O
more	O
easily	O
and	O
rapidly	O
understand	O
protein	O
structure	O
validation	O
reports	O
.	O
</s>
