Information Technology Reference
In-Depth Information
Table 1.
Additive model* for the binding affinity prediction to the I-A
b
allele.
P1
P2
P3
P4
P5
P6
P7
P8
P9
A
-0.016
-0.008
0.265
-0.115
0.066
-0.442
0.050
0.447
-0.034
C
0.000
0.083
0.037
-0.051
0.090
0.050
0.216
0.079
-0.139
D
-0.065
0.000
-0.067
0.000
0.000
0.107
-0.077
-0.041
-0.203
E
-0.028
-0.129
0.000
0.000
0.000
0.000
0.000
-0.048
0.000
F
0.000
0.000
0.000
-0.283
0.000
0.000
0.000
0.000
0.000
G
-0.286
-0.039
0.050
-0.011
0.000
0.000
-0.003
0.000
-0.067
H
-0.003
-0.013
0.000
0.000
0.000
0.000
0.000
0.213
0.000
I
-0.043
0.090
-0.364
-0.090
0.000
-0.244
-0.351
0.000
-0.069
K
0.094
0.000
0.000
0.000
-0.069
0.000
0.000
0.000
0.000
L
0.000
-0.215
-0.110
0.094
-0.162
0.000
-0.003
-0.242
0.066
M
0.008
-0.067
0.000
0.258
0.223
0.154
0.017
-0.027
0.082
N
0.000
0.298
0.000
0.042
-0.003
-0.069
0.064
-0.097
-0.455
P
0.100
0.000
0.032
0.090
0.030
0.201
0.080
0.000
0.280
Q
-0.013
0.000
-0.235
0.000
0.000
0.000
0.000
-0.067
-0.051
R
0.164
-0.286
0.066
0.122
-0.233
0.120
0.213
-0.229
0.216
S
-0.051
0.090
0.161
0.036
-0.078
0.041
-0.125
0.000
0.213
T
0.054
0.151
0.079
-0.060
0.233
0.000
-0.079
0.012
0.161
V
-0.069
-0.048
0.000
0.064
0.000
0.000
0.000
0.000
0.000
W
0.000
0.000
-0.029
0.000
-0.097
-0.003
0.000
0.000
0.000
Y
0.155
0.092
0.116
-0.097
0.000
0.085
0.000
0.000
0.000
*Constant = 6.044; 0.000 represents positions where amino acids are absent.
4.2.5.2 CoMSIA Method
Five physicochemical descriptors (Steric, Electrostatic, Hydrophobic, Hydrogen
Bond Donor and Acceptor) were evaluated using a probe atom placed within a 3D
grid. The atom had a radius of 1 Å and charge, hydrophobic interaction, hydrogen
bond donor and acceptor properties all equal to +1. The grid was extended beyond
the molecular dimensions by 4.0 Å in the X, Y, and Z directions. The spacing be-
tween probe points within the grid was set at 2.0 Å and was increased in steps of 0.5
Å. CoMSIA analysis for each allele was carried out using PLS (Young 2001) and
models were then validated via the LOO-CV method as previously described.
4.2.5.3 CoMSIA Maps
The results of the non-cross-validated CoMSIA models were displayed as contour
maps, with each physicochemical descriptor highlighted in different colors, reflect-
ing favorable or disfavorable changes in the peptide structure and its influence on
MHC binding. These maps were created using the standard deviation coefficient
option based on actual values. The CoMSIA steric bulk map is shown using green
(more bulk is favored) and yellow (less bulk is disfavored) contours. The electro-
static potential map is shown with blue (negative potential is disfavored) and red
(negative potential is favored) contours. CoMSIA hydrophobic interaction fields are
colored yellow (where hydrophobic interaction enhances affinity) and white (where
