Biomedical Engineering Reference
In-Depth Information
Table 4.1
Overview of impact of NMR restraint parameters and ROSETTA all-atom force-field on de novo structure.
Radius of
Interaction
Illustration
panel (Fig. 4.4)
Restraint type
Geometry
Instructiveness
Resolution
Challenges
NOESY
a
medium-range
A
distance
good
medium
assignment errors
RDC
b
global (via
alignment)
B
orientation
medium
medium
suitable alignment
conditions
PRE
long-range
C
distance
good
low
spin-label placement
PCS
c
long-range
B + C
distance/orientation
medium
medium
Spin-label placement,
PCS assignment
CS
b
short-range
D
torsion/contacts
low
high
not instructive
(ROSETTA)
d
high
e
not instructive
force-field errors
a
CASD benchmark, OFL unpublished results.
b
Proteins solved with CS-ROSETTA (Raman et al.
26
).
c
Benchmark of Proteins solved with PCS data, Schmitz
et al.
127 d
Benchmark of 111 proteins (Tyka et al.
47
).
e
RAAFF has high resolution, but in some unfavourable cases it can yield wrong answers. Cross-validation of
the obtained structures is required.
short-range
(Figure 4.3)
torsion/contacts
low
