An efficient visualization tool
for the analysis of protein
mutation matrices
Maria Pamela C. David, Carlo M. Lapid and Vincent
Ricardo M. Daria
Computational Science Research Center
University of the Philippines, Diliman
Outline



Visualization
A crash course on protein structure, function
and engineering
Protein mutation matrices




Generation
Data
Visualization
Applications of visualization
Visualization
Visualization
Visualization
Visualization
“Our species relies on vision over all other senses”
(about half of the human brain is devoted directly or
indirectly to vision)


“We learn about 11% audibly and 83% visually”

~50% of our brain gets involved in visual processing

Other perceptual channels can be used :
- They work in parallel as long as they don’t conflict
- In a conflict, the visual channel will dominate
Crash course on protein structure and
engineering
Protein mutations?
Protein mutation/substitution matrices

Analysis of evolving sequences/sequences
with high variability

Would have applications in artificial protein
design
Matrix generation
A
D
G
E
G
G
G
S T
W
K I
Y
E
L
R
K
T D
R
Matrix generation
A
D
G
E
G
G
S T
W
K I
Y
E
L
R
K
T D
R
G
Physico-chemical properties
Hydrophilicity
Size and Polarizability
Charge and polarity
T→I
D→G
R→E
S→L
S→K
W→R
T→D
Note:
1. Alignment should be good
2. Primer-derived sequences should be removed
Replaced residues, increasing hydrophilicity
Sample mutation matrix
Replacement residues, increasing hydrophilicity
W
L
F
I
M
V
Y
P
A
T
C
Q
G
K
S
H
N
E
R
D
W
0
0
0
0
1
37
3
0
36
0
2
1
4
0
0
35
25
0
0
0
L
2
0
59
225
155
76
0
26
73
36
37
110
40
4
149
2
4
110
7
76
F
36
6
0
1
0
3
3
0
46
0
0
0
79
2
4
38
37
39
0
3
I
41
92
7
0
148
235
35
0
0
143
0
0
39
49
24
1
74
0
73
2
M
36
32
72
15
0
50
0
0
3
3
0
37
26
10
5
0
2
1
64
4
V
1
84
36
0
2
0
73
0
15
41
0
1
4
39
43
266
75
60
0
0
Y
0
36
0
2
0
1
0
1
53
2
2
38
0
39
97
41
35
4
37
37
P
0
1
0
0
0
0
2
0
0
0
0
1
0
0
166
0
0
36
2
0
A
0
8
68
47
34
130
0
1
0
74
0
0
43
6
68
0
0
119
37
91
T
0
37
3
50
0
80
2
35
51
0
0
3
0
4
40
35
97
95
1
2
C
0
0
1
26
0
36
35
0
0
0
0
0
0
0
26
0
4
5
0
0
Q
0
3
0
36
1
38
36
1
3
0
24
0
1
3
4
2
39
150
13
70
G
25
7
75
39
0
0
79
0
87
2
25
3
0
37
44
3
32
41
1
39
K
0
55
49
47
29
4
36
0
0
29
0
114
81
0
7
0
47
140
394
40
S
2
103
0
5
0
4
40
110
112
96
135
5
114
42
0
0
239
5
63
111
H
0
0
0
4
2
88
4
0
2
0
2
194
0
6
2
0
33
37
0
8
N
0
160
2
43
3
2
3
0
1
8
4
32
9
90
159
10
0
151
76
124
E
1
149
1
6
4
38
2
0
3
75
0
41
159
137
39
2
85
0
9
135
R
0
43
39
2
0
1
1
0
1
54
8
2
97
236
93
0
78
49
0
58
D
4
37
2
3
39
4
76
3
2
73
1
1
125
93
122
4
123
44
4
0
Image equivalent
Lower
hydrophilicity
Higher
hydrophilicity
Tool 1: Matrix scaling
W L F
I
M V
Y
P
A
T C Q G
K S
H N E
R D
Tool 2: Matrix comparison
Find mutations exclusive to either matrix
W L F
I
M
V Y P A T C Q G K
Matrix 1
S H N
E R
D
W L F
I
M
V Y P A T C Q G K
Matrix 2
S H N
E R
D
Tool 2: Matrix comparison
W L F
I
M
V Y P A T C Q G K
S H N
E R
D
Matrix 2 only
Matrix 1 only
Application 1: antibody engineering
Complementarity
Determining
Region
FRamework
Application 1: antibody engineering
W L F
I
M
V Y P A T C Q G K
CDR mutations
S H N
E R
D
W L F
I
M
V Y P A T C Q G K
FR mutations
S H N
E R
D
Application 1: antibody engineering
S T
W
K I
Y
E
L
R
G
K
T D
D
K
T I
A
D
G
E
G
G
Engineered antibody
R
R
D
Application 2: vaccine design
Application 2: vaccine design
Lower
hydrophilicity
Higher
hydrophilicity
Application 3: biosensor design
Application 3: biosensor design
Smaller
residues
Larger
residues
Other advantages of visualization
Conclusion

Visualization plays a key role in analysis



Key applications of protein mutation matrix
visualization



Quicker elucidation of patterns
Find those that were not immediately obvious
Evolution studies
Protein engineering
Image manipulation and analysis techniques
may be applied to images
Current activities + future targets

Matrix generation tool development

Prototype hosted at the CSRC site

Migrate from Matlab to open source software
(i.e. Scilab/Octave + PERL/Tcl/Tk)

Offer full matrix generation + visualization
package online
T
H
A
N
K
Y
O
U
!
Q
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