Project name: AAV1_1mer_M1

Status: done

Started: 2026-10-21 17:40:55
Settings
Chain sequence(s) DGVGNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIANNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRTQNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWTGASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGASNTALDNVMITDEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYSTGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYLTRPL input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:05)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/e4d55551d9092c/tmp/folded.pdb                 (00:03:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:16)
Show buried residues

Minimal score value
-4.1432
Maximal score value
2.298
Average score
-0.5283
Total score value
-273.6529

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
17 D A -2.4697
18 G A -1.2729
19 V A 0.3474
20 G A -0.6410
21 N A -1.6926
22 A A -1.2741
23 S A -1.3944
24 G A -1.1519
25 N A -1.0865
26 W A -0.2304
27 H A -1.1824
28 C A -0.9345
29 D A -1.7703
30 S A -0.8564
31 T A -0.1598
32 W A 0.0758
33 L A 0.2936
34 G A -1.0450
35 D A -2.1375
36 R A -1.2686
37 V A 0.0000
38 I A -0.3866
39 T A 0.0000
40 T A 0.0000
41 S A 0.0000
42 T A 0.0000
43 R A 0.0000
44 T A 0.4430
45 W A 0.0000
46 A A 0.6932
47 L A 0.0000
48 P A 0.0770
49 T A -0.2087
50 Y A -0.1796
51 N A -0.6176
52 N A -0.9729
53 H A -0.2030
54 L A 0.3672
55 Y A -0.0726
56 K A -1.1185
57 Q A -0.8019
58 I A 0.2354
59 S A 0.0262
60 S A 0.0000
61 A A -0.2673
62 S A -0.2814
63 T A -0.5771
64 G A -0.8951
65 A A -1.1349
66 S A -1.5451
67 N A -2.3787
68 D A -2.3298
69 N A -2.1878
70 H A -1.7170
71 Y A -0.0833
72 F A 0.4224
73 G A 0.0000
74 Y A 0.3151
75 S A -0.1841
76 T A 0.0000
77 P A 0.0000
78 W A 0.0000
79 G A 0.0000
80 Y A 0.0000
81 F A 0.0000
82 D A 0.0000
83 F A 0.0000
84 N A 0.0000
85 R A -0.5392
86 F A 0.0000
87 H A 0.0000
88 C A 0.0000
89 H A 0.0000
90 F A 0.0000
91 S A -1.0457
92 P A -1.3969
93 R A -2.4965
94 D A -1.7709
95 W A 0.0000
96 Q A -2.0662
97 R A -2.5543
98 L A 0.0000
99 I A 0.0000
100 N A -1.0217
101 N A -1.9413
102 N A 0.0000
103 W A -0.8650
104 G A 0.0000
105 F A 0.0000
106 R A -0.8570
107 P A 0.0000
108 K A -1.9749
109 R A -1.9636
110 L A 0.0000
111 N A -0.9684
112 F A 0.0000
113 K A -1.0160
114 L A 0.0000
115 F A 0.0000
116 N A -1.0869
117 I A 0.0000
118 Q A -1.0776
119 V A 0.0000
120 K A -0.5508
121 E A -0.1951
122 V A 0.4055
123 T A 0.1787
124 T A -0.5063
125 N A -1.7842
126 D A -2.1018
127 G A -0.9327
128 V A 0.4944
129 T A 0.3906
130 T A 0.6415
131 I A 0.8791
132 A A -0.0797
133 N A -1.1210
134 N A -0.6295
135 L A 0.3350
136 T A -0.0807
137 S A 0.0000
138 T A 0.0000
139 V A 0.0000
140 Q A 0.0000
141 V A 0.0000
142 F A 0.0000
143 S A -0.4409
144 D A 0.0000
145 S A -1.3382
146 E A -2.2824
147 Y A -1.5173
148 Q A -1.3874
149 L A 0.0000
150 P A 0.2261
151 Y A 0.0221
152 V A 0.2072
153 L A 0.0000
154 G A -0.5120
155 S A -0.6408
156 A A -0.8124
157 H A -1.4664
158 Q A -1.6497
159 G A -0.6792
160 C A -0.4637
161 L A 0.0000
162 P A -0.0122
163 P A -0.0869
164 F A 0.6208
165 P A 0.0628
166 A A -0.1518
167 D A -0.5188
168 V A 1.2588
169 F A 0.0000
170 M A 1.3493
171 I A 0.0000
172 P A -0.2966
173 Q A -0.3397
174 Y A 0.0000
175 G A -0.0153
176 Y A 0.0000
177 L A 1.9692
178 T A 1.2169
179 L A 0.2800
180 N A -0.7713
181 N A -1.8616
182 G A -1.6340
183 S A -1.1899
184 Q A -1.4924
185 A A -0.9740
186 V A -0.8685
187 G A -1.0993
188 R A -1.6724
189 S A -0.4455
190 S A 0.5536
191 F A 1.4750
192 Y A 1.1201
193 C A 0.9129
194 L A 0.0000
195 E A -0.1667
196 Y A 1.0420
197 F A 0.2669
198 P A -0.2128
199 S A -0.4744
200 Q A -1.1174
201 M A -0.2064
202 L A 0.0000
203 R A -1.8378
204 T A -1.3780
205 G A 0.0000
206 N A -2.0201
207 N A -1.7327
208 F A 0.0000
209 T A -0.4805
210 F A -0.0895
211 S A -0.5341
212 Y A -0.5499
213 T A -1.3373
214 F A 0.0000
215 E A -2.2488
216 E A -2.2416
217 V A 0.0000
218 P A -0.4707
219 F A 0.0792
220 H A 0.0000
221 S A -0.0073
222 S A 0.0000
223 Y A -0.3041
224 A A -0.7270
225 H A -0.8940
226 S A -0.9311
227 Q A -1.2194
228 S A -1.1633
229 L A 0.0000
230 D A -1.5326
231 R A -1.4428
232 L A -0.4353
233 M A -0.1699
234 N A 0.0621
235 P A 0.4618
236 L A 1.8291
237 I A 1.7325
238 D A -0.6727
239 Q A -0.0837
240 Y A 1.1681
241 L A 0.9896
242 Y A 1.8059
243 Y A 1.4629
244 L A 1.7475
245 N A 0.2924
246 R A -0.7229
247 T A -1.1432
248 Q A -2.9843
249 N A -2.8785
250 Q A -2.5607
251 S A -1.6317
252 G A -1.7597
253 S A -1.1823
254 A A -1.7847
255 Q A -2.9441
256 N A -3.5122
257 K A -3.2606
258 D A -1.6996
259 L A 1.0863
260 L A 0.9564
261 F A 2.2980
262 S A 0.6888
263 R A -0.4539
264 G A 0.0000
265 S A -0.2206
266 P A 0.0802
267 A A 0.0062
268 G A 0.0231
269 M A -0.0731
270 S A -0.0774
271 V A 0.8479
272 Q A 0.0000
273 P A -0.3272
274 K A -1.1148
275 N A -1.2090
276 W A 0.2766
277 L A 0.6039
278 P A 0.4045
279 G A 0.0000
280 P A 0.3506
281 C A 0.0000
282 Y A 0.1068
283 R A -1.1396
284 Q A 0.0000
285 Q A -1.5315
286 R A -1.8697
287 V A -1.5384
288 S A 0.0000
289 K A -1.7239
290 T A -1.6897
291 K A -2.5969
292 T A -1.9750
293 D A -2.3570
294 N A -2.5768
295 N A -2.7052
296 N A -2.6303
297 S A -1.8013
298 N A -1.6280
299 F A -0.7266
300 T A -0.0670
301 W A 0.3369
302 T A -0.0424
303 G A -0.3993
304 A A -0.1099
305 S A -0.0250
306 K A 0.1444
307 Y A 0.5028
308 N A -0.9490
309 L A -0.0049
310 N A -1.4872
311 G A -1.4462
312 R A -1.9022
313 E A -1.4624
314 S A -0.3286
315 I A 0.3191
316 I A 0.2621
317 N A -0.7479
318 P A 0.0000
319 G A 0.1369
320 T A 0.1656
321 A A 0.2331
322 M A 0.0000
323 A A 0.0000
324 S A 0.0000
325 H A 0.0000
326 K A -3.5929
327 D A -4.1432
328 D A -3.9716
329 E A -3.6950
330 D A -3.9789
331 K A -2.6218
332 F A 0.0000
333 F A -1.2187
334 P A 0.0000
335 M A -0.4833
336 S A -0.3324
337 G A 0.0000
338 V A 0.0000
339 M A 0.0000
340 I A 1.3694
341 F A 0.2816
342 G A -1.1102
343 K A -2.2143
344 E A -2.3733
345 S A -1.7616
346 A A -1.6388
347 G A -1.2528
348 A A -0.6158
349 S A -0.9440
350 N A -1.3891
351 T A -1.0627
352 A A -0.7456
353 L A -0.6967
354 D A -1.6826
355 N A -1.5306
356 V A -0.5355
357 M A 0.0000
358 I A 0.4658
359 T A 0.0000
360 D A -1.2179
361 E A 0.0000
362 E A -2.5745
363 E A -1.8131
364 I A 0.0000
365 K A -2.3821
366 A A 0.0000
367 T A 0.0000
368 N A 0.0000
369 P A -0.6744
370 V A -0.9583
371 A A 0.0000
372 T A -1.5423
373 E A -2.1897
374 R A -2.1669
375 F A -0.7850
376 G A -0.7605
377 T A -0.1565
378 V A 1.1057
379 A A 1.1434
380 V A 1.7711
381 N A 0.6085
382 F A 1.0175
383 Q A -1.0880
384 S A -1.0471
385 S A -1.1692
386 S A -1.0484
387 T A -1.3450
388 D A -2.2423
389 P A -1.0712
390 A A -0.0237
391 T A 0.3755
392 G A -0.1097
393 D A -1.4397
394 V A -0.9621
395 H A -1.4300
396 A A -0.4039
397 M A -0.0519
398 G A -0.0807
399 A A 0.4085
400 L A 0.6082
401 P A 0.2155
402 G A 0.1250
403 M A 0.6375
404 V A 0.9471
405 W A 0.2814
406 Q A -0.4309
407 D A -0.4186
408 R A 0.0000
409 D A 0.0000
410 V A 0.0000
411 Y A 0.0000
412 L A 0.0000
413 Q A 0.0000
414 G A 0.0000
415 P A -0.3849
416 I A 0.0000
417 W A 0.0000
418 A A -0.5618
419 K A -1.3399
420 I A 0.0000
421 P A -1.4599
422 H A -1.9453
423 T A -1.7302
424 D A -2.3827
425 G A -1.4323
426 H A -0.5448
427 F A 1.2445
428 H A -0.0059
429 P A -0.1630
430 S A 0.0061
431 P A 0.2524
432 L A 0.9835
433 M A 0.4382
434 G A 0.0000
435 G A 0.0088
436 F A 0.0000
437 G A -0.8101
438 L A 0.0000
439 K A -2.3495
440 N A -2.2913
441 P A 0.0000
442 P A 0.0000
443 P A 0.0000
444 Q A 0.0000
445 I A 0.0000
446 L A 0.0000
447 I A 0.0000
448 K A 0.0000
449 N A 0.0000
450 T A 0.2037
451 P A 0.0365
452 V A 0.3673
453 P A 0.0834
454 A A -0.3133
455 N A -1.3304
456 P A -0.9201
457 P A -0.8440
458 A A -0.7491
459 E A -1.0232
460 F A 0.8806
461 S A 0.0344
462 A A 0.0347
463 T A -0.5151
464 K A -1.4516
465 F A -0.2619
466 A A -0.1822
467 S A -0.2892
468 F A 0.2935
469 I A 0.6249
470 T A 0.1482
471 Q A 0.0000
472 Y A 0.2940
473 S A 0.0000
474 T A 0.0240
475 G A 0.0000
476 Q A -0.3165
477 V A 0.0000
478 S A -0.6302
479 V A 0.0000
480 E A -1.2221
481 I A 0.0000
482 E A -1.3492
483 W A 0.0000
484 E A -1.3554
485 L A 0.0000
486 Q A -1.8381
487 K A -2.3548
488 E A -2.3060
489 N A -2.5395
490 S A -2.0748
491 K A -2.3472
492 R A -1.6272
493 W A -0.0588
494 N A -0.5412
495 P A -0.2829
496 E A 0.1578
497 V A 1.2949
498 Q A -0.0403
499 Y A -0.2582
500 T A -0.4279
501 S A -0.6730
502 N A -0.8826
503 Y A 0.2896
504 A A -0.3976
505 K A -1.6066
506 S A -1.0676
507 A A -0.7845
508 N A -1.0016
509 V A 0.4521
510 D A -0.4639
511 F A -0.1011
512 T A 0.4564
513 V A 0.3988
514 D A -1.1324
515 N A -2.1055
516 N A -1.8572
517 G A -1.0722
518 L A -0.1474
519 Y A -0.0055
520 T A -0.2743
521 E A -0.9013
522 P A -0.8099
523 R A -0.8117
524 P A -0.3339
525 I A 0.0000
526 G A -0.2265
527 T A 0.0000
528 R A 0.0000
529 Y A 0.3595
530 L A 0.0000
531 T A -0.4919
532 R A -1.4628
533 P A -0.7921
534 L A 0.0214
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Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.

pH
Average A3D Score
Max A3D Score
4.0 -0.1211 4.2925 View CSV PDB
4.5 -0.1673 4.2773 View CSV PDB
5.0 -0.2217 4.2607 View CSV PDB
5.5 -0.2763 4.2435 View CSV PDB
6.0 -0.323 4.2263 View CSV PDB
6.5 -0.3554 4.209 View CSV PDB
7.0 -0.3735 4.1918 View CSV PDB
7.5 -0.382 4.175 View CSV PDB
8.0 -0.3844 4.1592 View CSV PDB
8.5 -0.3801 4.146 View CSV PDB
9.0 -0.3668 4.1369 View CSV PDB