CASP8

Targets
387 388 389 390
391 392 393 394
395 396 397 398
399 400 401 402
403 404 405 406
407 408 409 410
411 412 413 414
415 416 417 418
419 420 421 422
423 424 425 426
427 428 429 430
431 432 433 434
435 436 437 438
439 440 441 442
443 444 445 446
447 448 449 450
451 452 453 454
455 456 457 458
459 460 461 462
463 464 465 466
467 468 469 470
471 472 473 474
475 476 477 478
479 480 481 482
483 484 485 486
487 488 489 490
491 492 493 494
495 496 497 498
499 500 501 502
503 504 505 506
507 508 509 510
511 512 513 514

Domain definition

For those wanting it quick: flat file with manual domain parse is here.

Proteins are composed of domains. Domains are usually defined as globular units in protein structures. Domains are somewhat separate from each other spatially and can recombine with each other in evolution to form various proteins. Each domain frequently carries out its own function, or the functional site may be formed at the domain interface. Analysis of domains is essential for understanding of proteins. However, while everyone agrees on the domain importance, opinions differ greatly about the criteria for domain definition, and existing software tools are inconsistent with each other in domain parse. Researchers think about domains from the position of structural compactness, sequence similarity and continuity, evolutionary origin, folding or function. Different criteria lead to different domain definitions. Nevertheless, our experience with protein sequence-structural analysis indicates that it might be possible to bring these criteria together for a biologically reasonable domain parse. We applied our conceptual view on protein domains to CASP8 targets. Domains defined here correspond to structurally compact evolutionary modules.

To define domains in a target we looked for similarity to other protein sequences and structures and self-similarity (internal duplications), structural compactness (globularity), presence of a hydrophobic core, and took into account sequence continuity. To define precise boundaries between domains, we inspected side-chain orientations and their interactions with domains. Domain parses by DOM, DOMAK, DomainParser, PDP and PUU, were also analyzed. We tried to attribute all residues in PDB to a domain rather than excluding extensions, loops and linkers, because if the residue is ordered, it should contribute to assessment of predictions. In some targets (e.g. T0435), certain regions protruded away from the PDB chain. These regions were frequently involved in a domain swap. In such cases, we defined globular domains with a swap, and also defined truncated domains with a swapped region removed. The following targets were affected by this:

In other cases, protruding regions did not participate in swaps, but were interacting with other chains in the crystals, e.g. in T0388. We removed such regions in domain definition to check whether the shorter domain is predicted more accurately. Text file with domain boundaries for all targets can be downloaded from here.

We did not take into account server predictions in defining domains, only sequence, structural and evolutionary considerations about targets were used. It might not be necessary to use these evolutionary domains for evaluation of all targets. See the discussion of whole chain vs. domain evaluation. In summary, comparison of domain-based predictions with whole chain predictions reveals that the following targets require domain-based evaluation: T0397, T0405, T0407, T0409, T0416, T0419, T0429, T0443, T0457, T0462, T0472, T0478, T0487, T0496, T0501, T0504, T0510, as for these targets server predictions for whole chains are much inferior to individual domain predictions. Only these targets are evaluated as domains in our combined domain evaluation tables. Predictions for other targets follow the general trend, are of a more similar quality for 'domain' and 'whole chain' and thus domain-based evaluation may not be necessary for them. Thus other targets are evaluated as whole chains in combined domain evaluation tables. These targets are considered to be single-domain proteins for evaluation. Although some of these targets are multi-domain proteins evolutionarily, domains do not move relatively to each other, are of the same prediction difficulty. Nevertheless, we compute evaluation scores on all domains shown in the table below, and these scores are available from individual target pages, e.g. T0497 page shows evaluation of whole chain (T0497), swapped domain (T0497_1s) and truncated domain with a swapped region removed (T0497_1).

In the table below, domains are marked by "_" followed by a domain number and preceded by a target name; "s" after the domain number denotes a swapped domain. Whole chains (no "_" in name) are given to show the residue range and mapping between target and PDB. Links to PyMOL scripts with domain definitions by various workers and programs are provided as well.

CASP8 targets and domainstext file
FM PyMOL
to see various
domain parses 		Type Category Range in target
(PDB modified to match
the target sequence) 		PyMOL
to see
domain 		PDB chain Range in PDB
T0387 PyMOL Human/Server CM_easy 2-84 PyMOL 2vsp A 2-84
T0388 PyMOL Server CM_easy 1-174 PyMOL 3cyn A 36-209
T0388_1     CM_easy 9-174 PyMOL   A 44-209
T0389 PyMOL Human/Server CM_medium 1-134 PyMOL 2vsw A 5-138
T0390 PyMOL Server CM_easy 29-160 PyMOL 3czu B 18-149
T0391 PyMOL Human/Server CM_hard 14-154 PyMOL 3d89 A 14-154
T0391_1     CM_medium 14-54,118-154 PyMOL   A 14-54,118-154
T0391_2     CM_medium 55-117 PyMOL   A 55-117
T0392 PyMOL Server CM_medium 8-104 PyMOL 2vsv A -15-594
T0392_1     CM_easy 24-104 PyMOL   A 514-594
T0393 PyMOL Human/Server CM_hard 4-263 PyMOL 3d1l A 4-263
T0393_1     CM_medium 4-163 PyMOL   A 4-163
T0393_2     CM_medium 164-263 PyMOL   A 164-263
T0393_2s     CM_hard 164-262 PyMOL   A,B A:164-182,B:183-262
T0394 PyMOL Server CM_hard 1-269 PyMOL 3dcy A -4-264
T0395 PyMOL Human/Server FR 1-304 PyMOL N/A A 1-304
T0395_1     CM_hard 1-197 PyMOL   A 1-197
T0395_2     FR 198-304 PyMOL   A 198-304
T0396 PyMOL Human/Server CM_easy 3-104 PyMOL N/A A 3-104
T0397 PyMOL Human/Server FR 1-150 PyMOL 3d4r A 1-150
T0397_1     FM 1-82 PyMOL   A 1-82
T0397_2     CM_medium 83-150 PyMOL   A 83-150
T0398 PyMOL Server CM_easy 1-291 PyMOL 3d4o A 1-291
T0398_1     CM_easy 1-128,273-291 PyMOL   A 1-128,273-291
T0398_2     CM_easy 129-272 PyMOL   A 129-272
T0399 PyMOL Human/Server FR 45-206 PyMOL 3d4e A 45-206
T0399_1     FR 45-128 PyMOL   A 45-128
T0399_2     CM_medium 129-206 PyMOL   A 129-206
T0400 PyMOL Server CM_easy 2-161 PyMOL 3d8p A 2-161
T0401 PyMOL Human/Server CM_hard 1-132 PyMOL 3d5p A 1-132
T0401_1     CM_hard 4-132 PyMOL   A 4-132
T0402 PyMOL Server CM_medium 1-126 PyMOL 3db0 A 1-126
T0404 PyMOL Server CM_easy 2-101 PyMOL 3dfe A 2-101
T0405 PyMOL Human/Server FM 2-282 PyMOL N/A A 2-282
T0405_1     FR 2-73 PyMOL   A 2-73
T0405_2     FM 74-282 PyMOL   A 74-182
T0406 PyMOL Server CM_medium 1-150 PyMOL 3di5 A 1-150
T0407 PyMOL Human/Server FR 22-363 PyMOL 3e38 A 22-363
T0407_1     CM_hard 22-266 PyMOL   A 22-266
T0407_2     FM 267-363 PyMOL   A 267-363
T0408 PyMOL Server CM_medium 8-104 PyMOL 3d7i A 8-104
T0409 PyMOL Human/Server FR 1-103 PyMOL 3d0f A 318-420
T0409_1     CM_hard 32-103 PyMOL   A 349-420
T0409_1s     FR 1-103 PyMOL   A,B B:318-348,A:349-420
T0410 PyMOL Server CM_easy 22-508 PyMOL 3d3l A 176-662
T0410_1     CM_easy 22-69,201-508 PyMOL   A 176-223,355-662
T0410_2     CM_easy 70-200 PyMOL   A 224-354
T0411 PyMOL Human/Server CM_medium 20-139 PyMOL 3d1p A 20-139
T0412 PyMOL Server CM_medium 1-176 PyMOL 3d3o A -2-173
T0413 PyMOL Human/Server FR 8-299 PyMOL 3d0k A 5-296
T0414 PyMOL Server CM_hard 3-140 PyMOL 3d0j A 0-137
T0414_1     CM_hard 9-140 PyMOL   A 6-137
T0415 PyMOL Human/Server CM_medium 1-109 PyMOL 3d6w A 106-214
T0415_1     CM_medium 1-54 PyMOL   A 106-159
T0415_2     CM_easy 55-109 PyMOL   A 160-214
T0416 PyMOL Server CM_hard 6-315 PyMOL 3d3q A 6-315
T0416_1     CM_easy 6-114,194-315 PyMOL   A 6-114,194-315
T0416_2     FR 115-193 PyMOL   A 115-193
T0417 PyMOL Human/Server CM_hard 26-184 PyMOL 3d3s A 1-159
T0418 PyMOL Server CM_easy 2-211 PyMOL 3d6j A 2-211
T0418_1     CM_easy 2-16,86-211 PyMOL   A 2-16,86-211
T0418_2     CM_easy 17-85 PyMOL   A 17-85
T0419 PyMOL Human/Server FM 1-496 PyMOL 3czp A 1-496
T0419_1     FR 1-237 PyMOL   A 1-237
T0419_2     FR 255-496 PyMOL   A 255-496
T0420 PyMOL Server CM_hard 1-178 PyMOL 3d5n A 1-178
T0421 PyMOL Human/Server FR 12-299 PyMOL 3czq A 12-299
T0422 PyMOL Server CM_medium 57-357 PyMOL 3d8b A 374-674
T0422_1     CM_medium 57-250,340-357 PyMOL   A 374-567,657-674
T0422_2     CM_easy 251-339 PyMOL   A 568-656
T0423 PyMOL Human/Server CM_easy 1-154 PyMOL 3d01 A 10-163
T0424 PyMOL Server CM_medium 6-347 PyMOL 3d37 A 6-347
T0424_1     CM_easy 6-93 PyMOL   A 6-93
T0424_2     CM_medium 94-178 PyMOL   A 94-178
T0424_3     CM_medium 179-207,278-347 PyMOL   A 179-207,278-347
T0424_4     CM_medium 208-277 PyMOL   A 208-277
T0425 PyMOL Human/Server CM_medium 1-181 PyMOL 3czx A 1-181
T0426 PyMOL Server CM_easy 22-283 PyMOL 3da2 A 0-261
T0427 PyMOL Human/Server CM_hard 1-422 PyMOL 3d3y A 1-422
T0427_1     CM_hard 1-230 PyMOL   A 1-230
T0427_2     CM_medium 231-422 PyMOL   A 231-422
T0428 PyMOL Server CM_easy 20-248 PyMOL 3d8h A 20-248
T0428_1     CM_easy 20-107,172-248 PyMOL   A 20-107,172-248
T0428_2     CM_easy 108-171 PyMOL   A 108-171
T0429 PyMOL Human/Server FR 20-176 PyMOL 3db3 A 127-283
T0429_1     CM_hard 20-100 PyMOL   A 127-207
T0429_2     FR 101-176 PyMOL   A 208-283
T0430 PyMOL Server FR 29-357 PyMOL 3dlz A 470-798
T0430_1     FR 29-166 PyMOL   A 470-607
T0430_2     FR 167-357 PyMOL   A 608-798
T0431 PyMOL Human/Server CM_medium 7-488 PyMOL 3dax A 24-505
T0432 PyMOL Server CM_easy 1-130 PyMOL 3dai A 979-1108
T0433 PyMOL Server CM_medium 1-199 PyMOL 3d7l A 1-199
T0434 PyMOL Human/Server CM_hard 11-205 PyMOL 3dal A -10-186
T0434_1     CM_hard 26-197 PyMOL   A 7-178
T0435 PyMOL Server CM_medium 4-141 PyMOL 3db5 A 4-141
T0435_1     CM_easy 14-141 PyMOL   A 14-141
T0435_1s     CM_medium 4-13,14-141 PyMOL   A,B B:4-13,A:14-141
T0436 PyMOL Server CM_hard 15-419 PyMOL 3d6k A 15-419
T0436_1     CM_medium 15-38,317-419 PyMOL   A 15-38,317-419
T0436_2     CM_hard 39-316 PyMOL   A 39-316
T0437 PyMOL Human/Server CM_medium 20-99 PyMOL 2k3i A 22-101
T0438 PyMOL Server CM_easy 2-430 PyMOL 3d3u A 2-430
T0438_1     CM_easy 2-185 PyMOL   A 2-185
T0438_2     CM_easy 186-430 PyMOL   A 186-430
T0440 PyMOL Human/Server CM_medium 1-275 PyMOL 3dcp A 1-275
T0441 PyMOL Server CM_medium 71-340 PyMOL 3d8u A 71-340
T0441_1     CM_medium 71-170,302-329 PyMOL   A 71-170,302-329
T0441_2     CM_easy 169-301,330-340 PyMOL   A 169-301,330-340
T0442 PyMOL Server CM_easy 11-266 PyMOL 3db9 A 11-266
T0442_1     CM_easy 11-124,233-266 PyMOL   A 11-124,233-266
T0442_2     CM_easy 131-232 PyMOL   A 131-232
T0443 PyMOL Human/Server FM 31-230 PyMOL 3dee A 31-230
T0443_1     FR 31-116 PyMOL   A 31-116
T0443_2     FR 117-230 PyMOL   A 117-230
T0444 PyMOL Server CM_easy 34-316 PyMOL 2vux A 30-312
T0445 PyMOL Server CM_medium 1-264 PyMOL 3dao A 1-264
T0445_1     CM_easy 1-81,190-264 PyMOL   A 1-81,190-264
T0445_2     CM_medium 82-189 PyMOL   A 82-189
T0446 PyMOL Human/Server CM_hard 8-124 PyMOL 3dcx A 0-124
T0447 PyMOL Server CM_easy 1-542 PyMOL 3do6 A 1-542
T0447_1     CM_easy 1-117,239-422 PyMOL   A 1-117,239-422
T0447_2     CM_easy 118-238 PyMOL   A 118-238
T0447_3     CM_easy 423-516 PyMOL   A 423-516
T0448 PyMOL Server CM_medium 18-230 PyMOL 3dc7 A 18-230
T0449 PyMOL Human/Server CM_hard 1-300 PyMOL 3dcd A 1-300
T0450 PyMOL Server CM_easy 1-549 PyMOL 3da1 A 1-549
T0450_1     CM_easy 1-62,168-247,343-406 PyMOL   A 1-62,168-247,343-406
T0450_2     CM_easy 63-101,163-167 PyMOL   A 63-101,163-167
T0450_3     CM_easy 102-162 PyMOL   A 102-162
T0450_4     CM_easy 248-342 PyMOL   A 248-342
T0450_5     CM_easy 407-549 PyMOL   A 407-549
T0451 PyMOL Human/Server CM_medium 1-133 PyMOL 3dmc A 1-133
T0452 PyMOL Server CM_easy 1-324 PyMOL 3do5 A 1-324
T0452_1     CM_easy 1-144,304-324 PyMOL   A 1-144,304-324
T0452_2     CM_easy 145-303 PyMOL   A 145-303
T0453 PyMOL Server CM_easy 5-91 PyMOL 3ded A 341-427
T0454 PyMOL Human/Server CM_hard 5-196 PyMOL 3dew A 5-196
T0454_1     CM_easy 5-56 PyMOL   A 5-56
T0454_2     CM_hard 57-196 PyMOL   A 57-196
T0455 PyMOL Server CM_easy 3-145 PyMOL 3ddv A 3-145
T0455_1     CM_easy 3-60 PyMOL   A 3-60
T0455_2     CM_easy 83-145 PyMOL   A 83-145
T0456 PyMOL Server CM_medium 15-284 PyMOL 3dfa A -2-267
T0456_1     CM_medium 15-104 PyMOL   A -2-87
T0456_2     CM_easy 105-284 PyMOL   A 89-267
T0457 PyMOL Human/Server FR 1-316 PyMOL 3dev A 1-316
T0457_1     CM_hard 1-194 PyMOL   A 1-194
T0457_2     FR 195-316 PyMOL   A 195-316
T0458 PyMOL Server CM_easy 11-89 PyMOL 3dex A 11-89
T0459 PyMOL Server CM_medium 1-109 PyMOL 3df8 A -2-106
T0459_1     CM_easy 26-109 PyMOL   A 23-106
T0459_1s     CM_medium 1-109 PyMOL   A,B B:-2-22,A:23-106
T0460 PyMOL Human/Server FR 1-103 PyMOL 2k4n A 1-103
T0461 PyMOL Server CM_easy 16-177 PyMOL 3dh1 A 12-173
T0462 PyMOL Human/Server FR 1-154 PyMOL 2k5i A 1-154
T0462_1     CM_medium 1-75 PyMOL   A 1-75
T0462_2     CM_medium 76-146 PyMOL   A 76-146
T0463 PyMOL Server CM_medium 3-219 PyMOL 3dhn A 3-219
T0464 PyMOL Human/Server CM_hard 16-88 PyMOL 2k5r A 16-88
T0465 PyMOL Human/Server FM 7-137 PyMOL 3dfd A 7-137
T0465_1     FR 21-137 PyMOL   A 21-137
T0466 PyMOL Human/Server FR 14-108 PyMOL 2k5d A 14-108
T0467 PyMOL Human/Server FR 8-94 PyMOL 2k5q A 8-94
T0468 PyMOL Human/Server FR 11-109 PyMOL 2k5w A 11-109
T0469 PyMOL Human/Server CM_medium 1-65 PyMOL 2k5e A 1-65
T0470 PyMOL Server CM_easy 2-214 PyMOL 3djb A 2-214
T0470_1     CM_easy 2-100 PyMOL   A 2-100
T0470_2     CM_easy 112-214 PyMOL   A 112-214
T0471 PyMOL Human/Server CM_hard 1-131 PyMOL 2k4m A 21-151
T0472 PyMOL Server CM_hard 1-110 PyMOL 2k49 A 1-110
T0472_1     CM_easy 2-50,102-110 PyMOL   A 2-50,102-110
T0472_2     CM_easy 51-101 PyMOL   A 51-101
T0473 PyMOL Human/Server CM_medium 1-68 PyMOL 2k53 A 1-68
T0474 PyMOL Human/Server CM_easy 7-52 PyMOL 2k5j A 7-52
T0475 PyMOL Server CM_medium 1-122 PyMOL 2k54 A 1-122
T0476 PyMOL Human/Server FR 1-88 PyMOL 2k5c A 8-95
T0477 PyMOL Server CM_medium 1-242 PyMOL 3dkp A 137-378
T0478 PyMOL Server FM 4-267 PyMOL 3d19 A 11-274
T0478_1     FR 4-137 PyMOL   A 11-144
T0478_2     FR 138-267 PyMOL   A 145-274
T0479 PyMOL Server CM_easy 6-130 PyMOL 3dkz A 39-163
T0480 PyMOL Human/Server CM_medium 17-50 PyMOL 2k4x A 17-50
T0481 PyMOL Server CM_medium 5-154 PyMOL 3dka A 5-154
T0482 PyMOL Human/Server FR 1-107 PyMOL 2k4v A 4-110
T0483 PyMOL Server CM_medium 9-293 PyMOL 3dls A 982-1266
T0483_1     CM_medium 9-110 PyMOL   A 982-1083
T0483_2     CM_easy 111-293 PyMOL   A 1084-1266
T0484 PyMOL Human/Server CM_easy 13-26 PyMOL 2k5k A 13-26
T0485 PyMOL Server CM_hard 1-218 PyMOL 3dlc A 1-218
T0485_1     CM_hard 5-216 PyMOL   A 5-216
T0486 PyMOL Server CM_easy 32-287 PyMOL 2vx2 A 45-300
T0486_1     CM_easy 32-230 PyMOL   A 45-243
T0486_2     CM_easy 231-287 PyMOL   A 244-300
T0487 PyMOL Human/Server FR 3-642 PyMOL 3dlb A 3-642
T0487_1     CM_hard 3-11,310-318,467-642 PyMOL   A 3-11,310-318,467-642
T0487_2     FR 12-25,97-176,266-309 PyMOL   A 12-25,97-176,266-309
T0487_3     CM_hard 26-96 PyMOL   A 26-96
T0487_4     FR 177-265 PyMOL   A 177-265
T0487_5     CM_hard 319-466 PyMOL   A 319-466
T0488 PyMOL Server CM_easy 1-95 PyMOL 2vwr A -1-428
T0488_1     CM_easy 1-90 PyMOL   A -1-423
T0489 PyMOL Human/Server FR 17-253 PyMOL 3dl1 A 17-253
T0490 PyMOL Server CM_medium 3-368 PyMOL 3dme A 3-368
T0490_1     CM_medium 3-49,148-228,318-368 PyMOL   A 3-49,148-228,318-368
T0490_2     CM_easy 50-88,143-147 PyMOL   A 50-88,143-147
T0490_3     CM_easy 89-142 PyMOL   A 89-142
T0490_4     CM_medium 229-317 PyMOL   A 229-317
T0491 PyMOL Server CM_easy 1-98 PyMOL 3dm4 A 1-98
T0492 PyMOL Human/Server CM_medium 1-73 PyMOL 2k5l A 1-73
T0493 PyMOL Human/Server CM_medium 3-172 PyMOL 3dmn A 596-765
T0494 PyMOL Server CM_medium 32-378 PyMOL 2vx3 A 135-481
T0494_1     CM_easy 32-137 PyMOL   A 135-240
T0494_2     CM_medium 138-378 PyMOL   A 241-481
T0495 PyMOL Human/Server FR 5-150 PyMOL 3dnx A 5-150
T0496 PyMOL Human/Server FM 4-178 PyMOL 3do9 A 4-178
T0496_1     FM 4-126 PyMOL   A 4-126
T0496_2     CM_medium 127-178 PyMOL   A 127-178
T0497 PyMOL Server CM_medium 1-145 PyMOL 3dmb A 1-145
T0497_1     CM_medium 1-133 PyMOL   A 1-133
T0497_1s     CM_medium 1-145 PyMOL   A,C A:1-133,C:134-145
T0498 PyMOL Human/Server CM_hard 7-54 PyMOL 2jws A 7-54
T0499 PyMOL Human/Server CM_easy 1-56 PyMOL 2jwu A 1-56
T0501 PyMOL Server FR 2-343 PyMOL 3dma A 2-343
T0501_1     CM_hard 2-214 PyMOL   A 2-214
T0501_2     CM_hard 215-343 PyMOL   A 215-343
T0502 PyMOL Server CM_medium 4-101 PyMOL 3dm3 A 4-101
T0503 PyMOL Server CM_medium 1-146 PyMOL 3dn7 A 1-146
T0504 PyMOL Server FM 1-208 PyMOL 3dlm A 1-208
T0504_1     CM_medium 1-61 PyMOL   A 1-61
T0504_2     FR 62-152 PyMOL   A 62-152
T0504_3     CM_easy 153-208 PyMOL   A 153-208
T0505 PyMOL Server CM_medium 6-280 PyMOL 3dnp A 3-277
T0505_1     CM_easy 6-85,200-280 PyMOL   A 3-82,197-277
T0505_2     CM_hard 86-199 PyMOL   A 83-196
T0506 PyMOL Server CM_hard 4-254 PyMOL 3dnh A 4-254
T0506_1     CM_medium 4-173 PyMOL   A 4-173
T0506_2     CM_medium 174-254 PyMOL   A 174-254
T0507 PyMOL Server CM_hard 1-142 PyMOL 3do8 A 1-142
T0508 PyMOL Server CM_easy 17-197 PyMOL 3dou A 17-197
T0509 PyMOL Server CM_medium 3-213 PyMOL 3dr5 A 3-213
T0510 PyMOL Server FR 1-279 PyMOL 3doa A 1-279
T0510_1     FR 1-165 PyMOL   A 1-165
T0510_2     CM_hard 166-235 PyMOL   A 166-235
T0510_3     FR 236-279 PyMOL   A 236-279
T0511 PyMOL Server CM_medium 1-271 PyMOL 3e03 A 3-273
T0512 PyMOL Server CM_hard 1-327 PyMOL 3dsm A 15-341
T0513 PyMOL Server FR 1-283 PyMOL 3dup A 1-283
T0513_1     CM_hard 1-15,115-283 PyMOL   A 1-15,115-283
T0513_2     FR 16-114 PyMOL   A 16-114
T0514 PyMOL Server FR 2-145 PyMOL 3dtd A 42-185