PFRMAT AL
TARGET T0089
AUTHOR 2000-8506-6614
METHOD Overview
METHOD 
METHOD The SAM_T99 results for this target, available from the CAFASP2 meta-server
METHOD (http://cafasp.bioinfo.pl/), were obtained from the SAM_T99 web server
METHOD (http://www.cse.ucsc.edu/research/compbio/HMM-apps/T99-query.html).
METHOD 
METHOD Fold recognition by the SAM_T99 server was performed using the SAM-T99 method
METHOD (which is similar to SAM_T98 [3]) using SAM version 3.1 [1], a refinement of 
METHOD the methods developed by this group for CASP3 [7].  This method attempts to
METHOD find and multiply align a set of homologs to a given sequence, then create an
METHOD HMM from that multiple alignment.
METHOD 
METHOD First, a set of sequence weights is determined from the alignment.  Next, 
METHOD Modelfromalign is used to build the model from the alignment and the 
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring 
METHOD of the sequences, using a reversed-sequence normalization feature.
METHOD 
METHOD The weighting method, detailed in publications [3,4],
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an
METHOD entropy method to set the final weights.
METHOD 
METHOD Alignment generation
METHOD 
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set
METHOD of very close homologs, and once to produce a set of possible homologs.
METHOD 
METHOD The method then uses multiple iterations of a selection, training, and 
METHOD alignment procedure.  Each iteration involves an initial alignment, a set 
METHOD of search sequences, a threshold value, and a transition regularizer. 
METHOD 
METHOD The first iteration uses a single sequence (or seed alignment) as the 
METHOD initial alignment and the close homologs found by BLASTP are used as the 
METHOD search set.  The threshold is set very strictly, so that only good matches 
METHOD to the sequence are considered.  This iteration uses a transition regularizer 
METHOD that was designed to match the gap costs used by BLASTP.
METHOD 
METHOD On subsequent iterations the input alignment is the output from the
METHOD previous iteration, the search set is the larger set of possible
METHOD homologs found by BLASTP, and the thresholds are gradually loosened.
METHOD The second through second-from-last iteration use a ``long-match''
METHOD transition regularizer, and the final iteration uses a transition regularizer 
METHOD trained on FSSP alignments.
METHOD 
METHOD 
METHOD Fold Recognition Submission Criteria For CAFASP2
METHOD 
METHOD The submitted alignments are a subset of the SAM_T99 results available
METHOD from the CAFASP2 meta-server. The CAFASP2 meta-server results are for a
METHOD query with a loose threshold E-value of 50.0, so not necessarily all the
METHOD database hits on the meta-server are submitted as official SAM-T99 predictions
METHOD for evaluation. For meta-server raw output with no filtered list of databse
METHOD hits, only the top hit is submitted.
METHOD 
METHOD References
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996.
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.  
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R.
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and 
METHOD     Genetics, Suppl. 1, 134-9, 1997.
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06,
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998.
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard,
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998.
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994.
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S.
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996.
METHOD [7] Karplus, K; Barrett, C; Cline, M; Diekhans, M; Grate, L; Hughey, R. 
METHOD     Predicting protein structure using only sequence information.
METHOD     Proteins, 1999, Suppl 3:121-5.
MODEL 1
PARENT 1hpm
T 11 V 7
S 12 G 8
I 13 I 9
D 14 D 10
I 15 L 11
G 16 G 12
S 17 T 13
R 18 T 14
Y 19 Y 15
I 20 S 16
K 21 C 17
G 22 V 18
L 23 G 19
V 24 V 20
L 25 F 21
R 28 Q 22
D 29 H 23
Q 30 G 24
E 31 K 25
W 32 V 26
E 33 E 27
A 34 I 28
L 35 I 29
A 36 G 34
F 37 N 35
S 38 R 36
S 39 T 37
V 40 T 38
K 41 P 39
S 42 S 40
R 43 Y 41
G 44 V 42
L 45 A 43
D 46 F 44
E 47 E 48
G 48 R 49
E 49 L 50
I 50 I 51
K 51 G 52
D 52 D 53
A 53 A 54
I 54 A 55
A 55 K 56
F 56 N 57
K 57 Q 58
E 58 V 59
S 59 A 60
V 60 M 61
N 61 N 62
T 62 N 65
L 63 T 66
L 64 V 67
K 65 F 68
E 66 D 69
L 67 A 70
E 68 K 71
E 69 R 72
Q 70 L 73
L 71 I 74
Q 72 G 75
K 73 R 76
S 74 R 77
L 75 F 78
R 76 D 79
S 77 A 81
D 78 V 82
F 79 V 83
V 80 Q 84
I 81 S 85
S 82 D 86
F 83 M 87
S 84 K 88
S 85 H 89
V 86 W 90
S 87 P 91
F 88 F 92
E 89 M 93
R 90 V 94
E 91 V 95
D 92 N 96
T 93 P 101
V 94 K 102
I 95 V 103
E 96 Q 104
R 97 V 105
D 98 E 106
F 99 Y 107
G 100 K 108
E 101 G 109
E 102 E 110
K 103 T 111
R 104 K 112
S 105 S 113
I 106 F 114
T 107 Y 115
L 108 P 116
D 109 E 117
I 110 E 118
L 111 V 119
S 112 S 120
E 113 S 121
M 114 M 122
Q 115 V 123
S 116 L 124
E 117 T 125
A 118 K 126
L 119 M 127
E 120 K 128
K 121 E 129
L 122 I 130
K 123 A 131
E 124 E 132
N 125 A 133
G 126 Y 134
K 127 L 135
K 155 G 136
I 156 K 137
A 157 T 138
I 158 V 139
E 159 T 140
Y 160 N 141
T 161 A 142
S 162 V 143
I 163 V 144
V 164 T 145
V 165 V 146
P 166 P 147
L 167 A 148
K 168 Y 149
V 169 F 150
Y 170 N 151
E 171 D 152
M 172 S 153
F 173 Q 154
Y 174 R 155
N 175 Q 156
F 176 A 157
L 177 T 158
Q 178 K 159
D 179 D 160
T 180 A 165
V 181 G 166
K 182 L 167
S 183 N 168
P 184 V 169
F 185 L 170
Q 186 R 171
L 187 I 172
K 188 I 173
S 189 N 174
S 190 E 175
L 191 P 176
V 192 T 177
S 193 A 178
T 194 A 179
A 195 A 180
E 196 I 181
G 197 A 182
V 198 Y 183
L 199 G 184
T 200 L 185
T 201 D 186
P 202 K 187
E 203 G 190
K 204 A 191
D 205 E 192
R 206 R 193
G 207 N 194
V 208 V 195
V 209 L 196
V 210 I 197
V 211 F 198
N 212 D 199
L 213 L 200
G 214 G 201
Y 215 G 202
N 216 G 203
F 217 T 204
T 218 F 205
G 219 D 206
L 220 V 207
I 221 S 208
A 222 I 209
Y 223 I 212
K 224 E 213
N 225 D 214
G 226 G 215
V 227 I 216
P 228 F 217
I 229 E 218
K 230 T 222
I 231 A 223
S 232 G 224
Y 233 D 225
V 234 T 226
P 235 H 227
V 236 L 228
G 237 G 229
M 238 G 230
K 239 E 231
H 240 D 232
V 241 F 233
I 242 D 234
K 243 N 235
D 244 R 236
V 245 M 237
S 246 V 238
A 247 N 239
V 248 H 240
L 249 F 241
D 250 I 242
T 251 A 243
S 252 E 244
F 253 F 245
E 254 K 246
E 255 A 266
S 256 C 267
E 257 E 268
R 258 R 269
L 259 A 270
I 260 K 271
I 261 R 272
T 262 T 273
H 263 L 274
G 264 S 275
N 265 S 276
A 266 S 277
V 267 T 278
Y 268 Q 279
N 269 A 280
E 273 S 281
E 274 I 282
E 275 E 283
I 276 I 284
Q 277 D 285
Y 278 S 286
R 279 L 287
G 280 Y 288
L 281 E 289
D 282 G 290
G 283 I 291
N 284 D 292
T 285 F 293
I 286 Y 294
K 287 T 295
T 288 S 296
T 289 I 297
T 290 T 298
A 291 R 299
K 292 A 300
K 293 R 301
L 294 F 302
S 295 E 303
V 296 E 304
I 297 L 305
I 298 N 306
H 299 A 307
A 300 D 308
R 301 L 309
L 302 F 310
R 303 R 311
E 304 G 312
I 305 T 313
M 306 L 314
S 307 D 315
K 308 P 316
S 309 V 317
K 310 E 318
K 311 K 319
F 312 A 320
F 313 L 321
R 314 R 322
E 315 D 323
V 316 A 324
E 317 K 325
A 318 L 326
K 319 D 327
I 320 K 328
V 321 S 329
E 322 Q 330
E 323 I 331
G 324 H 332
E 325 D 333
V 332 I 334
V 333 V 335
L 334 L 336
T 335 V 337
G 336 G 338
G 337 G 339
G 338 S 340
A 339 T 341
K 340 R 342
I 341 I 343
P 342 P 344
R 343 K 345
I 344 I 346
N 345 Q 347
E 346 K 348
L 347 L 349
A 348 L 350
T 349 Q 351
E 350 D 352
V 351 F 353
F 352 F 354
N 363 N 355
S 364 G 356
D 365 K 357
R 366 E 358
P 367 L 359
S 368 N 360
I 369 K 361
I 370 S 362
N 377 I 363
D 378 N 364
P 379 P 365
S 380 D 366
F 381 E 367
A 382 A 368
A 383 V 369
A 384 A 370
F 385 Y 371
G 386 G 372
N 387 A 373
V 388 A 374
F 389 V 375
A 390 Q 376
V 391 A 377
S 392 A 378
E 393 I 379
N 394 L 380
P 395 S 381
Y 396 G _
E 397 D _
E 398 K _
TER
END