Project name: jrk_1AKL

Status: done

Started: 2026-02-08 17:35:07
Chain sequence(s) A: GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:09)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:52:20)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:52:24)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:52:27)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:52:31)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:52:35)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:52:39)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:52:43)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:52:46)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:52:50)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:52:54)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:52:58)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:53:02)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:53:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:53:15)
[INFO]       Main:     Simulation completed successfully.                                          (01:53:19)
Show buried residues

Minimal score value
-3.46
Maximal score value
1.9658
Average score
-0.5382
Total score value
-252.934

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
1 G A -1.9704
2 R A -2.3951
3 S A -1.8552
4 D A -2.6405
5 A A -2.1093
6 Y A 0.0000
7 T A -2.2206
8 Q A -2.2344
9 V A 0.0000
10 D A -2.1259
11 N A -2.0626
12 F A -0.9730
13 L A -1.0540
14 H A -1.6078
15 A A -0.8555
16 Y A 0.0000
17 A A -1.1657
18 R A -1.8682
19 G A -1.7181
20 G A -1.8445
21 D A -2.3549
22 E A -1.6331
23 L A -0.1379
24 V A 0.1802
25 N A -1.0680
26 G A -1.2100
27 H A -1.6352
28 P A -1.0990
29 S A 0.0000
30 Y A 0.0000
31 T A 0.0000
32 V A 0.0000
33 D A -3.0961
34 Q A -2.6854
35 A A 0.0000
36 A A 0.0000
37 E A -3.4600
38 Q A -2.4087
39 I A 0.0000
40 L A -2.0563
41 R A -2.8628
42 E A -2.1966
43 Q A -1.3266
44 A A -1.2454
45 S A -1.0333
46 W A 0.0000
47 Q A -2.2516
48 K A -2.5379
49 A A 0.0000
50 P A -1.6874
51 G A -1.9817
52 D A -2.1408
53 S A -1.5766
54 V A 0.0000
55 L A 0.0000
56 T A -0.3184
57 L A 0.0000
58 S A -0.1598
59 Y A 0.0000
60 S A 0.0000
61 F A -1.0813
62 L A 0.0000
63 T A -1.5150
64 K A -2.6156
65 P A -2.2440
66 N A -2.7690
67 D A -2.7553
68 F A -1.3598
69 F A 0.0000
70 N A -2.5565
71 T A -1.3961
72 P A -0.5909
73 W A 0.0000
74 K A -1.3011
75 Y A -0.0180
76 V A 0.0000
77 S A -0.8227
78 D A -1.1694
79 I A 0.1878
80 Y A 0.0000
81 S A -0.3390
82 L A -0.7953
83 G A -1.5595
84 K A -1.8792
85 F A -1.0433
86 S A -0.6002
87 A A -0.6961
88 F A 0.0000
89 S A -0.6378
90 A A -0.7985
91 Q A -1.6196
92 Q A -1.3009
93 Q A -0.9198
94 A A -0.8222
95 Q A -0.9142
96 A A 0.0000
97 K A -0.7639
98 L A -0.1272
99 S A 0.0000
100 L A 0.0000
101 Q A -0.4683
102 S A 0.0000
103 W A 0.0000
104 S A -0.6081
105 D A 0.0000
106 V A 0.0000
107 T A 0.0000
108 N A -0.9919
109 I A 0.0000
110 H A -0.4599
111 F A 0.5982
112 V A 0.6134
113 D A -1.1895
114 A A -1.1555
115 G A -1.5482
116 Q A -2.0973
117 G A -1.8283
118 D A -2.0118
119 Q A -1.8377
120 G A 0.0000
121 D A -1.0470
122 L A 0.0000
123 T A 0.0000
124 F A 0.0000
125 G A 0.0000
126 N A 0.1740
127 F A 0.0000
128 S A -0.1751
129 S A 0.0000
130 S A 0.1521
131 V A -0.3134
132 G A -0.5337
133 G A -0.5402
134 A A 0.0000
135 A A 0.1685
136 F A 0.0000
137 A A 0.0000
138 F A 0.0000
139 L A 0.0000
140 P A -0.9917
141 D A -1.3506
142 V A -0.3726
143 P A -0.9804
144 D A -1.8516
145 A A -1.0405
146 L A 0.0000
147 K A -1.3122
148 G A 0.0000
149 Q A 0.0000
150 S A 0.0000
151 W A 0.0000
152 Y A 0.6824
153 L A 0.0000
154 I A 1.0681
155 N A -0.1019
156 S A -0.1366
157 S A 0.1018
158 Y A 0.5543
159 S A 0.3246
160 A A 0.2041
161 N A 0.1768
162 V A 0.2366
163 N A 0.0000
164 P A -1.1305
165 A A -0.8005
166 N A -0.7821
167 G A -0.4448
168 N A 0.0000
169 Y A 0.3996
170 G A -0.1557
171 R A -0.2778
172 Q A 0.0000
173 T A 0.0000
174 L A 0.0000
175 T A 0.0000
176 H A 0.0000
177 E A 0.0000
178 I A 0.0000
179 G A 0.0000
180 H A 0.0000
181 T A 0.0000
182 L A 0.0000
183 G A 0.0000
184 L A 0.0000
185 S A 0.0000
186 H A 0.0000
187 P A 0.0000
188 G A -1.1600
189 D A -1.6633
190 Y A -0.8689
191 N A -0.9267
192 A A 0.0000
193 G A -1.4851
194 E A -2.1683
195 G A -0.9980
196 D A 0.0000
197 P A 0.0000
198 T A 0.0000
199 Y A 0.4694
200 A A 0.1431
201 D A -0.0791
202 A A -0.0212
203 T A 0.1769
204 Y A 0.0000
205 A A -0.1561
206 E A -0.7111
207 D A 0.0000
208 T A 0.0000
209 R A 0.0000
210 A A 0.0000
211 Y A 0.0000
212 S A 0.0000
213 V A 0.0000
214 M A 0.0000
215 S A 0.0000
216 Y A 0.2160
217 W A -0.2490
218 E A -1.4558
219 E A 0.0000
220 Q A -2.5663
221 N A -2.2453
222 T A 0.0000
223 G A -1.6840
224 Q A -1.6490
225 D A -2.4889
226 F A 0.0000
227 K A -2.3101
228 G A 0.0000
229 A A 0.0000
230 Y A 0.0000
231 S A 0.0000
232 S A 0.0000
233 A A 0.0000
234 P A 0.0000
235 L A 0.0000
236 L A 0.0000
237 D A 0.0000
238 D A 0.0000
239 I A 0.0000
240 A A 0.0000
241 A A 0.0000
242 I A 0.0000
243 Q A -1.6014
244 K A -2.3493
245 L A -0.8291
246 Y A -0.8710
247 G A -1.0808
248 A A -0.5911
249 N A 0.0671
250 L A 1.1823
251 T A 0.0869
252 T A -0.3802
253 R A 0.0000
254 T A -1.2459
255 G A -1.5816
256 D A -1.7728
257 T A 0.0000
258 V A 0.4782
259 Y A 0.0000
260 G A 0.0000
261 F A 1.2048
262 N A -0.1790
263 S A -0.5509
264 N A -1.6916
265 T A 0.0000
266 E A -1.8579
267 R A 0.0000
268 D A -0.7741
269 F A 0.0000
270 Y A 0.0000
271 S A -0.2625
272 A A -0.4300
273 T A -0.5659
274 S A -0.6551
275 S A 0.0000
276 S A -1.1124
277 S A -1.0365
278 K A -1.2477
279 L A 0.0000
280 V A 0.0000
281 F A 0.0000
282 S A 0.0000
283 V A 0.0000
284 W A 0.0000
285 D A 0.0979
286 A A -0.4656
287 G A -0.8139
288 G A -1.5821
289 N A -1.9741
290 D A 0.0000
291 T A -0.6106
292 L A 0.0000
293 D A -0.2833
294 F A 0.3115
295 S A 0.1541
296 G A 0.0004
297 F A 0.5262
298 S A -0.2956
299 Q A 0.0000
300 N A -1.6465
301 Q A 0.0000
302 K A -1.0400
303 I A 0.0000
304 N A 0.0000
305 L A 0.0000
306 N A 0.0000
307 E A -1.3436
308 K A 0.0000
309 A A 0.0000
310 L A -0.0662
311 S A 0.0000
312 D A -1.2587
313 V A 0.0000
314 G A -1.7493
315 G A -1.6783
316 L A 0.0000
317 K A -2.3147
318 G A 0.0000
319 N A 0.0000
320 V A 0.0000
321 S A 0.0000
322 I A 0.0000
323 A A 0.0000
324 A A -0.7938
325 G A -0.7440
326 V A -0.5050
327 T A -0.7000
328 V A 0.0000
329 E A -1.5083
330 N A -1.1247
331 A A 0.0000
332 I A 0.0000
333 G A 0.0000
334 G A 0.0000
335 S A 0.0000
336 G A -0.9987
337 S A -1.4203
338 D A 0.0000
339 L A 0.0000
340 L A 0.0000
341 I A 0.0000
342 G A 0.0000
343 N A -1.6211
344 D A -2.0010
345 V A -1.2113
346 A A 0.0000
347 N A -1.3014
348 V A 0.0000
349 L A 0.0000
350 K A -1.5832
351 G A 0.0000
352 G A -0.4439
353 A A -0.4105
354 G A -0.9492
355 N A 0.0000
356 D A -2.0435
357 I A 0.0000
358 L A 0.0000
359 Y A 0.0000
360 G A 0.0000
361 G A 0.0000
362 L A 0.0000
363 G A -1.3735
364 A A -1.0339
365 D A -1.6812
366 Q A -1.4320
367 L A 0.0000
368 W A -0.7475
369 G A 0.0000
370 G A 0.0000
371 A A 0.0000
372 G A -0.8183
373 A A -1.2130
374 D A 0.0000
375 T A -1.0513
376 F A 0.0000
377 V A 0.0000
378 Y A 0.0000
379 G A 0.0000
380 D A 0.0000
381 I A 0.0000
382 A A -0.8617
383 E A -1.6030
384 S A 0.0000
385 S A -0.6317
386 A A -0.3434
387 A A -0.2602
388 A A -0.3638
389 P A -0.6204
390 D A 0.0000
391 T A -0.9615
392 L A 0.0000
393 R A -1.2953
394 D A -1.0979
395 F A 1.0596
396 V A 1.4598
397 S A 0.3089
398 G A -0.3064
399 Q A -1.1507
400 D A 0.0000
401 K A -0.7236
402 I A 0.0000
403 D A 0.0000
404 L A 0.0000
405 S A 0.0000
406 G A -1.1727
407 L A 0.0000
408 D A -1.4083
409 A A -1.0337
410 F A -0.2094
411 V A 0.9187
412 N A -0.2228
413 G A -1.1156
414 G A -0.9179
415 L A -0.5426
416 V A 0.0000
417 L A 0.0000
418 Q A 0.2296
419 Y A 0.7407
420 V A 0.6602
421 D A -1.2016
422 A A 0.0000
423 F A 1.4684
424 A A 0.1618
425 G A -1.0321
426 K A -1.9338
427 A A -0.9087
428 G A -0.7408
429 Q A -0.6807
430 A A 0.0000
431 I A 1.9658
432 L A 1.4559
433 S A 0.5712
434 Y A 0.2245
435 D A -1.6167
436 A A -1.2118
437 A A -0.8421
438 S A -1.0970
439 K A -1.8762
440 A A -1.0329
441 G A 0.0000
442 S A 0.1459
443 L A 0.0000
444 A A -0.1168
445 I A 0.0000
446 D A -2.1830
447 F A -1.5188
448 S A -1.1813
449 G A -1.1973
450 D A -1.2140
451 A A -0.8463
452 H A 0.0000
453 A A 0.0000
454 D A -1.8745
455 F A 0.0000
456 A A -0.6963
457 I A 0.0000
458 N A -0.3537
459 L A 0.0000
460 I A -0.3920
461 G A -0.3877
462 Q A 0.0000
463 A A 0.0000
464 T A -0.4426
465 Q A -0.2418
466 A A 0.3667
467 D A -0.1516
468 I A 0.0000
469 V A 1.3200
470 V A 0.6829
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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, -0.5382 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_9 -0.5382 View CSV PDB
model_3 -0.5406 View CSV PDB
model_4 -0.5474 View CSV PDB
model_0 -0.5477 View CSV PDB
model_5 -0.5517 View CSV PDB
model_1 -0.5519 View CSV PDB
CABS_average -0.5597 View CSV PDB
model_10 -0.5599 View CSV PDB
model_6 -0.5656 View CSV PDB
model_7 -0.5687 View CSV PDB
model_8 -0.5705 View CSV PDB
model_11 -0.5769 View CSV PDB
model_2 -0.5975 View CSV PDB
input -0.6076 View CSV PDB