Probabilistic Chemical Shift Assignment of the
Backbone
a) Probabilistic
Chemical Shift Assignment in PINE Format.
ADAPT-NMR generates a probabilistic assignment of
chemical shift for every residue. This means that it is possible for some
residues to have more than one candidate spin systems. In these cases, an
associated probability is assigned to each candidate spin system assigned to
the residue. The sum of all probabilities always adds to one. See
the sample output shown in the table below.
The probability for the system is shown columns marked with P(H,N). A probability of 1 indicates an extremely confident
assignment. A value of 0 columns indicates that no candidate spin system with a
reasonable probability was found to match that residue. When more than one
possibility is detected (see row 2), the structure in the columns 3-5 for the
given residue is repeated and the alternative probabilities and associated
chemical shift assignments for 1H and 15N are specified. The last column, P(no_assignment), represent the probability that no
spin systems in the data set can be associated with that residue (see row
20). The table shows portions of the
backbone assignment with computed probabilities.
Residue_Name
P(H,N) H N
CO CA CB
P(H,N) H N P(H,N) H
N P(H,N) H
N P(no_assignment)
1
MET 0.000 0.000
0.00 0.00 55.40
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 1.000
2
GLN 0.602 7.851
120.31 0.00 55.40
0.00 0.396 8.623
123.91 0.001 8.041
123.94 0.000 0.000
0.00 0.000
3
ILE 1.000 7.851
120.31 0.00 59.63
42.06 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
4
PHE 1.000 8.593
118.52 0.00 55.11
41.23 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
5
VAL 1.000 9.301
121.32 0.00 60.51
34.23 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
6
LYS 1.000 8.868
127.82 0.00 54.57
34.46 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
7
THR 1.000 8.733
115.59 0.00 60.56
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
8
LEU 1.000 9.113
121.46 0.00 57.51
41.92 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
9
THR 1.000 7.635
105.98 0.00 61.49
69.09 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
10
GLY 1.000 7.807
109.28 0.00 45.35
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
11
LYS 1.000 7.262
121.99 0.00 56.27
33.37 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
12
THR 1.000 8.648
120.71 0.00 62.45
69.80 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
13
ILE 1.000 9.508
127.78 0.00 60.02
40.76 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
14
THR 1.000 8.743
121.88 0.00 62.12
69.67 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
15
LEU 1.000 8.717
125.16 0.00 52.74
46.90 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
16
GLU 1.000 8.121
122.53 0.00 54.91
29.66 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
17
VAL 1.000 8.924
117.59 0.00 58.40
36.34 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
18
GLU 1.000 8.640
119.33 0.00 52.71
30.83 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
19
PRO 0.000 0.000
0.00 0.00 65.31
31.88 0.000 0.000
0.00 0.000 0.000
0.00 0.000 0.000
0.00 0.000
20
SER 0.966 7.022
103.50 0.00 57.41
63.38 0.003 8.623
123.91 0.000 0.000
0.00 0.000 0.000
0.00 0.031
...
...
...
b) Overall
Picture of the Assignment.
A jpg figure
is also sent to the user that demonstrates the overall picture of the
assignment. The graphic represents the amino acid sequence with colored bars
indicating the assignment probability: green bars indicate assignments with
probabilities > 99%; a cyan bar indicates probabilities between 85%-99%; a
yellow bar indicates probabilities between 50%-85%; and a red bar indicates assignments
with probabilities less thatn 50%. Finally a gray bar
indicates "no assignment" has higher probability than any other
candidate spin systems.
