PFRMAT AL 
TARGET T0062 
AUTHOR 7648-2940-6918 
REMARK  
METHOD We align a target sequence with structurally aligned sequences 
METHOD (i.e., multiple structure alignment), where a multiple structure 
METHOD alignment is computed from results of pairwise structure alignments 
METHOD for similar structures.  
METHOD Pairwise structure alignments are computed using a computer 
METHOD program STRALIGN [1] developed by the group-leader and they are 
METHOD combined into a multiple structure alignment using a method like 
METHOD center-star alignment. 
METHOD A simple dynamic programming procedure (Smith-Waterman like procedure) 
METHOD is used for computing an alignment between a target sequence and 
METHOD the aligned sequences. 
METHOD Finally, an alignment between a target and one of the aligned 
METHOD sequences (i.e., template sequence) is extracted and refined. 
METHOD Human knowledge is also used to find template structures and 
METHOD to refine alignments. 
METHOD 
METHOD [1] T. Akutsu: Protein structure alignment using dynamic programming 
METHOD and iterative alignment, IEICE Transactions on Information and Systems, 
METHOD vol. E79-D, pp. 1629--1636, 1996. 
METHOD 
METHOD Program code of STRALIGN is available via 
METHOD http://www.hgc.ims.u-tokyo.ac.jp/service/tooldoc/stralign/intro.html 
MODEL  1 
PARENT 1que 
L   3    F  21 
S   4    I  22 
C   5    G  23 
K   6    K  24 
V   7    V  25 
T   8    I  26 
S   9    S  27 
V  10    N  28 
E  11    E  29 
A  12    P  30 
I  13    L  31 
T  16    I  39 
V  17    V  40 
Y  18    Q  41 
R  19    H  42 
V  20    I  43 
R  21    K  44 
I  22    F  45 
V  23    L  47 
P  24    T  48 
F  30    Y  54 
R  31    I  55 
A  32    E  56 
G  33    G  57 
Q  34    Q  58 
Y  35    S  59 
L  36    I  60 
M  37    G  61 
V  38    I  62 
V  39    I  63 
M  40    P  64 
D  41    P  65 
E  42    G  66 
R  43    V  67 
D  44    D  68 
K  45    K  69 
R  46    R  77 
P  47    L  78 
F  48    Y  79 
S  49    S  80 
M  50    I  81 
A  51    A  82 
S  52    S  83 
T  53    T  84 
P  54    R  85 
D  55    H  86 
G  58    K  93 
F  59    T  94 
I  60    I  95 
E  61    S  96 
L  62    L  97 
H  63    C  98 
I  64    V  99 
L  81    I 124 
K  82    E 125 
D  83    G 127 
H  84    S 128 
Q  85    E 129 
I  86    V 130 
V  87    K 131 
V  88    I 132 
D  89    T 133 
I  90    G 134 
P  91    P 135 
H  92    V 136 
G  93    G 137 
E  94    K 138 
A  95    E 139 
W  96    M 140 
L  97    L 141 
R  98    L 142 
D  99    P 143 
D 100    D 144 
E 102    E 147 
R 103    A 148 
P 104    N 149 
M 105    V 150 
I 106    I 151 
L 107    M 152 
I 108    L 153 
A 109    A 154 
G 110    T 155 
G 111    G 156 
T 112    T 157 
G 113    G 158 
F 114    I 159 
S 115    A 160 
Y 116    P 161 
A 117    M 162 
R 118    R 163 
S 119    T 164 
I 120    Y 165 
L 121    L 166 
L 122    W 167 
T 123    R 168 
A 124    M 169 
L 125    F 170 
D 132    F 186 
I 133    S 187 
T 134    W 188 
I 135    L 189 
Y 136    V 190 
W 137    F 191 
G 138    G 192 
G 139    V 193 
R 140    P 194 
E 141    T 196 
E 142    P 197 
Q 143    N 198 
H 144    I 199 
L 145    L 200 
Y 146    Y 201 
L 148    K 202 
C 149    E 203 
E 150    E 204 
L 151    L 205 
E 152    E 206 
A 153    E 207 
L 154    I 208 
S 155    Q 209 
L 156    Q 210 
K 157    K 211 
H 158    Y 212 
P 159    P 213 
L 161    F 216 
Q 162    R 217 
V 163    L 218 
V 164    T 219 
P 165    Y 220 
V 166    A 221 
V 167    I 222 
E 168    S 223 
Q 169    R 224 
P 170    E 225 
G 173    G 231 
W 174    G 232 
R 175    R 233 
G 176    M 234 
R 177    Y 235 
T 178    I 236 
G 179    Q 237 
T 180    D 238 
V 181    R 239 
L 182    V 240 
T 183    A 241 
A 184    E 242 
V 185    H 243 
L 186    A 244 
Q 187    D 245 
D 188    Q 246 
H 189    L 247 
G 190    W 248 
T 191    Q 249 
L 192    L 250 
A 193    I 251 
I 197    T 258 
Y 198    Y 259 
I 199    I 260 
A 200    C 261 
G 201    G 262 
R 202    L 263 
F 203    R 264 
E 204    G 265 
M 205    M 266 
A 206    E 267 
K 207    E 268 
I 208    G 269 
A 209    I 270 
R 210    D 271 
D 211    A 272 
L 212    A 273 
F 213    L 274 
C 214    S 275 
S 215    A 276 
E 216    A 277 
R 217    A 278 
TER 
END 
