Project name: RBD_WT

Status: done

Started: 2026-06-15 15:38:08
Chain sequence(s) E: TNLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLDSKVGGNYNYLYRLFRKSNLKPFERDISTEIYQAGSTPCNGVEGFNCYFPLQSYGFQPTNGVGYQPYRVVVLSFELLHAPATVCG
input PDB
Selected Chain(s) E
Distance of aggregation 10 Å
FoldX usage No
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with E chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:35:29)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:35:30)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:35:31)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:35:33)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:35:33)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:35:34)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:35:35)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:35:36)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:35:37)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:35:38)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:35:39)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:35:40)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:35:41)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:35:44)
[INFO]       Main:     Simulation completed successfully.                                          (00:35:46)
Show buried residues
Minimal score value
-3.5727
Maximal score value
3.0738
Average score
-0.2278
Total score value
-44.1959
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
333 T E -0.3610
334 N E -0.5561
335 L E 0.8029
336 C E 0.2236
337 P E -0.3482
338 F E -0.4063
339 G E -0.9631
340 E E -1.8442
341 V E -0.8170
342 F E 0.0000
343 N E -1.2575
344 A E -0.7263
345 T E -0.7648
346 R E -1.0298
347 F E 0.0620
348 A E 0.0000
349 S E 0.0653
350 V E 0.0000
351 Y E 0.0000
352 A E -0.1816
353 W E -0.4373
354 N E -1.8582
355 R E -3.2459
356 K E -3.5727
357 R E -3.1300
358 I E 0.0000
359 S E -1.2503
360 N E -1.2223
361 C E 0.0000
362 V E 0.3328
363 A E -0.3806
364 D E -1.3699
365 Y E 0.0000
366 S E -0.2766
367 V E -0.0041
368 L E 0.0000
369 Y E 0.4684
370 N E -0.3021
371 S E -0.2661
372 A E -0.4121
373 S E -0.4502
374 F E -0.0318
375 S E -0.3897
376 T E -0.4455
377 F E 0.1905
378 K E -0.1690
379 C E 0.6876
380 Y E 1.1549
381 G E 0.3138
382 V E 0.0000
383 S E -0.4553
384 P E -0.8810
385 T E -1.3243
386 K E -2.0004
387 L E -1.1829
388 N E -1.6171
389 D E -1.9526
390 L E -0.1232
391 C E 0.3804
392 F E 0.0000
393 T E 0.0000
394 N E -0.8134
395 V E 0.0000
396 Y E -1.5574
397 A E 0.0000
398 D E 0.0000
399 S E 0.0000
400 F E 0.0000
401 V E 0.0000
402 I E 0.0000
403 R E -0.6232
404 G E 0.0000
405 D E -2.2606
406 E E 0.0000
407 V E 0.0000
408 R E -3.1484
409 Q E -2.5973
410 I E 0.0000
411 A E -1.3165
412 P E -1.1571
413 G E -1.6493
414 Q E -2.5020
415 T E 0.0000
416 G E -1.9993
417 K E -2.1451
418 I E 0.0000
419 A E -1.5110
420 D E -1.7298
421 Y E -0.4043
422 N E 0.0000
423 Y E 0.0000
424 K E -1.4193
425 L E 0.0000
426 P E -0.9623
427 D E -1.6160
428 D E -0.2465
429 F E 1.2664
430 T E 0.6610
431 G E 0.0000
432 C E 0.0000
433 V E 0.0000
434 I E 0.0000
435 A E 0.0000
436 W E 0.0000
437 N E -0.5924
438 S E 0.0000
439 N E -1.5028
440 N E -1.7576
441 L E -1.2675
442 D E 0.0000
443 S E -0.9025
444 K E -0.3088
445 V E 0.9896
446 G E 0.0300
447 G E -0.1903
448 N E -0.0912
449 Y E 0.2219
450 N E -0.6913
451 Y E 0.0000
452 L E 0.4400
453 Y E 0.0000
454 R E 0.0000
455 L E 0.6003
456 F E 0.9332
457 R E 0.0000
458 K E -1.2137
459 S E -0.3948
460 N E -0.2238
461 L E 0.6181
462 K E -0.1857
463 P E -0.1783
464 F E 0.2863
465 E E 0.0000
466 R E -0.9561
467 D E -0.3190
468 I E 0.4633
469 S E 0.5023
470 T E 1.0630
471 E E 0.7277
472 I E 2.2374
473 Y E 0.0000
474 Q E -0.0013
475 A E 0.4870
476 G E -0.2055
477 S E -0.0573
478 T E -0.0258
479 P E -0.0202
480 C E 0.1477
481 N E -0.9809
482 G E -0.4509
483 V E 0.7097
484 E E -0.1658
485 G E 0.8529
486 F E 1.9187
487 N E 0.0000
488 C E 1.3232
489 Y E 2.5552
490 F E 3.0738
491 P E 1.6389
492 L E 0.9860
493 Q E -0.5172
494 S E -0.4746
495 Y E 0.0000
496 G E -0.0170
497 F E 0.8037
498 Q E 0.0000
499 P E -0.2238
500 T E -0.2152
501 N E 0.0908
502 G E 0.6472
503 V E 1.4891
504 G E 0.1713
505 Y E 1.0761
506 Q E 0.0000
507 P E 0.0000
508 Y E 0.0000
509 R E 0.0000
510 V E 0.0000
511 V E 0.0000
512 V E 0.0000
513 L E 0.0000
514 S E 0.0000
515 F E 0.0000
516 E E 0.8908
517 L E 1.9143
518 L E 1.7825
519 H E 0.1540
520 A E 0.2614
521 P E -0.0410
522 A E 0.1741
523 T E -0.5738
524 V E 0.0000
525 C E 0.1534
526 G E -0.8084
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.2278 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_10 -0.2278 View CSV PDB
model_8 -0.3799 View CSV PDB
model_7 -0.3801 View CSV PDB
model_4 -0.4141 View CSV PDB
input -0.4212 View CSV PDB
model_6 -0.4414 View CSV PDB
model_3 -0.4525 View CSV PDB
CABS_average -0.461 View CSV PDB
model_11 -0.4629 View CSV PDB
model_2 -0.4918 View CSV PDB
model_5 -0.5358 View CSV PDB
model_1 -0.5518 View CSV PDB
model_9 -0.5559 View CSV PDB
model_0 -0.6379 View CSV PDB