SVM?????????? ?????????????

1
SVM???????????????????????

• ????? ????? ????
• ??? ???? ????
• ?????????????????
• ?????????????????????

2
??

• ???????
• ????????
• Protein Data Bank (PDB)
• Support Vector Machine (SVM)
• ????????
• ??
• ???

3
???????

• ??????? ????? ?????
• ????????

4
Calmodulin
Ca??????
?
?

• Ca??????
• ????????????

• Ca????????
• ???????????

Ca2/calmodulin
????
Ca??????????? (1DMO)
Ca??????????(3CLN)
5
??????????

• ???????????????
• ???????????

• NMR (Nuclear Magnetic Resonance)
• X???????

???????????

• ???????
• ??????????????

6
???????????????

• ??????????????
• ??????????????????

?????????????????
????????????????????
7
?????

• ???????????

ARG CYS THR HIS TYP ALA GLY SER
PRO GLN GLN LEU CYS ARG PRO MET
PRO HIS ARG LEU GLN CYS TYP SER
?????? (??????????)
??????????
8
Protein Data Bank (PDB)

• ??????????????????????
• ????NMR,X?????????
• ???????????? (???55,000)

PDB???????
9
Support Vector Machine (SVM)

• Vapnik???????
• 2????????????
• ??????????????
• ???????
• ????????
• ????????
• ????????

?????
????
????????
10
?????????

1. PDB???????PDB???????
2. ???????????
3. ?? ? ?????????
4. ??

PDB file
??
??
??
Training data file
?? ??
SVM
SVM
PDB(Protein Data Bank)
Model file
11
?????????

1. PDB???????PDB???????
2. ???????????
3. ?? ? ?????????
4. ??

PDB file
??
??
??
Training data file
?? ??
SVM
SVM
PDB(Protein Data Bank)
Model file
12
PDB?????????

• ????
• X???????
• ?????????
• ???????????
• ???????????

????????? ?????????? ??PDB???????
PDB file
??
??
??
Training data file
?? ??
SVM
SVM
PDB(Protein Data Bank)
Model file
13
?????????

1. PDB???????PDB???????
2. ???????????
3. ?? ? ?????????
4. ??

PDB file
??
??
??
Training data file
SVM
?? ??
SVM
PDB(Protein Data Bank)
Model file
14
?????????????

• ?????????????
• ?????????????????a???????????????????
• ?PDB?????????
• PDB?????CONECT????????????????

15
???????????????????? (1/2)

1. ??????a??????????
2. ?????-a???????????
3. ?????????

Metal atom
Alpha carbon atom
(M_x, M_y, M_z)
(Ca_x, Ca_y, Ca_z)
16
???????????????????? (2/2)

1. ????????????????????
2. ??????????????
3. ????????????? (??????)
4. ????????????

ALA0, ARG2,, GLX0
HIS
CYS
ARG
PHE
GLN
ARG
SER
MET
?????????
ALA
10 22 210 220 10 21 210 221 10 21
210 220
PHE
?????
TRP
TRP
17
????????????????????

1. ??????????????????????
2. ?????????????????
3. ????????????????
4. ??????????????
5. ?????????????
6. ????????????

?????????
10 22 210 220 10 21 210 221 10 21
210 220
18
?????????

1. PDB???????PDB???????
2. ???????????
3. ?? ? ?????????
4. ??

PDB file
??
??
??
Training data file
?? ??
SVM
SVM
PDB(Protein Data Bank)
Model file
19
?????????

1. PDB???????PDB???????
2. ???????????
3. ?? ? ?????????
4. ??

PDB file
??
??
??
Training data file
?? ??
SVM
SVM
PDB(Protein Data Bank)
Model file
20
?????

• LIBSVM (A Library for Support Vector Machine)
• Lin??????????SVM??????
• SVM???
• C-SVC (C-Support Vector Classification)
• ??????????
• e-SVR (e-Support Vector Regression)
• ???????????
• Gaussian Kernel
• ?????
• Grid search ? Cross Validation ?????

21
??1???????(????)

• ?????????? (4Å,5Å,6Å)
• ??????? (7??,9??,11??)

????????????????(?) ? ???????(?)
7?? 9?? 11??
4.0Å 37.2 62.1 71.1
5.0Å 31.8 46.4 73.5
6.0Å 35.7 47.1 72.0
7?? 9?? 11??
4.0Å 89.0 82.0 87.0
5.0Å 100 100 100
6.0Å 99.0 100 100
22
????1

• ?????????????????????

??????
?????(?)???(?)????
Zn 7?? 9?? 11??
4.0Å 37.2 62.1 71.1
5.0Å 31.8 46.4 73.5
6.0Å 35.7 47.1 72.0

• ?????????
• - ???????
• ????????
• - ????????

Zn 7?? 9?? 11??
4.0Å 89.0 82.0 87.0
5.0Å 100 100 100
6.0Å 99.0 100 100

• ??????????
• ?????????

23
????1

• ?????????????????????

???????
?.?????????
Zn 7?? 9?? 11??
4.0Å 37.2 62.1 71.1
5.0Å 31.8 46.4 73.5
6.0Å 35.7 47.1 72.0

• 4Å????????? - ????????

??????
??(Å) 4.0 5.0 6.0
???? 23 153 318
Zn 7?? 9?? 11??
4.0Å 89.0 82.0 87.0
5.0Å 100 100 100
6.0Å 99.0 100 100
24
??2???????(????)

• ??????? (7??,9??,11??)
• ????(II)

??????????????(?) ? ?(II)????(?)
Zn 7?? 9?? 11??
?????? 96.7 100 100
??????? 86.0 100 100
Fe(II) 7?? 9?? 11??
?????? 41.5 22.6 42.5
??????? 100 100 100
25
????2

• ???????????????????

???????
Zn 7?? 9?? 11??
?????? 96.7 100 100
??????? 86.0 100 100

• Fe(II)???????? - ???????? (Zn 216,Fe(II)
  11)

Fe(II) 7?? 9?? 11??
?????? 41.5 22.6 42.5
??????? 100 100 100
????
26
??3?????? (1/2)

• ??????????????? (??2)
• e-SVR?????????
• ??????????? (0 1???) 1 ??????????????
• ?????? (0.95 0.50 0.05??)
• (???) gt (???) ???????

(???) gt (???)
(???) gt (???)
27
??3?????? (2/2)

• ???????????
• 7, 25, 29, 37, 40, 53, 57, 65, 68, 81, 85 (?11??)
• ???0.95
• 11???7???????????
• ????4?????????

1A1F????????????
??? ????
0.95 613 3445 4859 6371
0.90 613 2545 4771 8090
0.85 613 2572 8090
0.80 614 2572 7990
7, 25, 29, 37, 40, 53, 57, 65, 68, 81, 85
7, 25, 29, 37, 40, 53, 57, 65, 68, 81, 85
7, 25, 29, 37, 40, 53, 57, 65, 68, 81, 85
7, 25, 29, 37, 40, 53, 57, 65, 68, 81, 85
28
????3

• ??????
• ??????????? (Zn, Fe(II) ??)
• ?????????
• ?????? (Pt?K ??)
• ?????????

1A1F????????????
??? ?????? (????) / (????)
0.95 613 3445 4859 6371 4/4
0.90 613 2545 4771 8090 4/4
0.85 613 2572 8090 3/3
0.80 614 2572 7990 3/3
29
???

• ??????????????????
• ???? ???????
• PDB???????????
• 2???????????????????????,??????
• SVM????????
• ??
• ????????????20???????
• ???????????????