Project name: 2lmndynamo

Status: done

Started: 2026-03-03 19:16:17
Chain sequence(s) A: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
C: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
B: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
E: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
D: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
G: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
F: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
I: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
H: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
K: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
J: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
L: GYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
input PDB
Selected Chain(s) A,C,B,E,D,G,F,I,H,K,J,L
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]                                                (00:00:02)
[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 all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:09:17)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (01:46:52)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (01:46:55)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (01:46:58)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (01:47:01)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (01:47:04)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (01:47:07)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (01:47:10)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (01:47:15)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (01:47:18)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (01:47:21)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (01:47:24)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (01:47:27)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (01:47:30)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (01:47:39)
[INFO]       Main:     Simulation completed successfully.                                          (01:47:48)
Show buried residues
Minimal score value
-3.2848
Maximal score value
4.0673
Average score
0.1452
Total score value
55.7479
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
9 G A -0.1374
10 Y A 0.3818
11 E A -0.8936
12 V A -0.3215
13 H A -1.6882
14 H A -2.6532
15 Q A -3.1500
16 K A -2.7189
17 L A -0.3611
18 V A 1.4583
19 F A 2.2249
20 F A 2.2197
21 A A 0.2887
22 E A -1.2570
23 D A -0.7408
24 V A 0.5874
25 G A -0.8447
26 S A -1.4604
27 N A -2.5082
28 K A -3.2848
29 G A -1.6649
30 A A -0.4597
31 I A 1.7076
32 I A 2.5873
33 G A 2.2532
34 L A 2.8544
35 M A 3.0158
36 V A 3.0975
37 G A 2.3562
38 G A 2.0215
39 V A 3.3808
40 V A 2.7965
9 G B -0.1039
10 Y B 0.8828
11 E B 0.0128
12 V B -0.1645
13 H B -1.3588
14 H B -2.1293
15 Q B -2.9610
16 K B -2.3923
17 L B 0.0000
18 V B 0.0000
19 F B 0.0000
20 F B 1.7227
21 A B -0.0187
22 E B -0.8395
23 D B 0.0000
24 V B 1.1302
25 G B -0.5599
26 S B -1.6030
27 N B -2.7191
28 K B -3.2429
29 G B -1.5292
30 A B -0.8023
31 I B 1.3167
32 I B 1.9751
33 G B 1.8992
34 L B 2.1331
35 M B 0.0000
36 V B 2.4466
37 G B 0.0000
38 G B 2.7146
39 V B 4.0673
40 V B 3.5328
9 G C 0.1496
10 Y C 0.8610
11 E C -0.0542
12 V C 0.0549
13 H C -0.7339
14 H C -1.4647
15 Q C -1.7808
16 K C -1.8037
17 L C 0.0000
18 V C 0.4581
19 F C 0.0000
20 F C 0.9981
21 A C -0.1521
22 E C -0.4945
23 D C 0.0000
24 V C 1.3812
25 G C 0.3195
26 S C -0.7086
27 N C -1.8561
28 K C -1.6073
29 G C -0.9415
30 A C 0.0000
31 I C 0.0000
32 I C 0.9165
33 G C 0.0000
34 L C 0.0000
35 M C 0.0000
36 V C 1.2205
37 G C 0.0000
38 G C 2.2822
39 V C 3.9495
40 V C 3.9569
9 G D -0.1371
10 Y D 0.6995
11 E D -0.1876
12 V D 0.1035
13 H D -0.9794
14 H D -1.3286
15 Q D -1.6782
16 K D -1.4782
17 L D 0.0000
18 V D 0.8613
19 F D 0.0000
20 F D 1.3315
21 A D -0.1825
22 E D -0.7082
23 D D -0.3419
24 V D 1.2718
25 G D 0.2641
26 S D 0.0000
27 N D 0.0000
28 K D 0.0000
29 G D -0.1590
30 A D 0.0000
31 I D 0.3238
32 I D 0.0000
33 G D 0.2270
34 L D 0.0000
35 M D 0.0000
36 V D 0.5232
37 G D 0.0000
38 G D 1.3168
39 V D 3.0098
40 V D 3.3221
9 G E -0.7651
10 Y E -0.6054
11 E E -1.6341
12 V E -0.8554
13 H E -1.4372
14 H E -1.7352
15 Q E -1.7918
16 K E -1.4337
17 L E 0.3942
18 V E 1.8927
19 F E 2.7578
20 F E 1.9972
21 A E 0.0382
22 E E -1.1884
23 D E -1.4846
24 V E -0.3939
25 G E -0.9998
26 S E -0.7935
27 N E -1.6998
28 K E -1.6967
29 G E -0.9847
30 A E 0.0000
31 I E 0.0000
32 I E 0.9684
33 G E 0.0000
34 L E 0.0000
35 M E 0.0000
36 V E 0.4761
37 G E 0.0000
38 G E 1.3733
39 V E 2.6802
40 V E 2.8821
9 G F -0.1492
10 Y F 0.0777
11 E F -1.6465
12 V F -0.9922
13 H F -1.7446
14 H F -2.1532
15 Q F -2.4074
16 K F -1.6881
17 L F 1.1767
18 V F 2.5400
19 F F 3.7677
20 F F 2.5102
21 A F 0.2367
22 E F -1.8041
23 D F -2.0236
24 V F 0.0580
25 G F -0.2859
26 S F -0.4864
27 N F -1.5323
28 K F 0.0000
29 G F -0.7621
30 A F -0.5099
31 I F 0.6699
32 I F 1.4873
33 G F 1.0740
34 L F 1.1619
35 M F 0.8492
36 V F 0.6667
37 G F 0.5052
38 G F 1.1592
39 V F 1.8898
40 V F 1.7379
9 G G -0.1724
10 Y G 0.1774
11 E G -1.1966
12 V G -0.9147
13 H G -1.8522
14 H G -2.4949
15 Q G -2.7960
16 K G -2.2427
17 L G 0.3517
18 V G 2.1004
19 F G 2.3945
20 F G 2.5518
21 A G 1.0135
22 E G -0.1132
23 D G 0.2362
24 V G 0.9590
25 G G -0.4463
26 S G -0.8994
27 N G -2.2708
28 K G -3.0332
29 G G -1.9343
30 A G -0.1343
31 I G 2.1191
32 I G 3.1954
33 G G 2.7214
34 L G 2.6036
35 M G 2.3837
36 V G 2.3760
37 G G 1.5412
38 G G 1.8430
39 V G 3.0067
40 V G 3.0018
9 G H -0.0906
10 Y H 0.7502
11 E H -0.0616
12 V H -0.3643
13 H H -0.8198
14 H H 0.0000
15 Q H -2.1458
16 K H -1.9207
17 L H -0.1489
18 V H 1.2780
19 F H 0.0000
20 F H 1.6587
21 A H 0.4597
22 E H -0.3638
23 D H 0.0000
24 V H 0.1216
25 G H -0.9045
26 S H -1.2990
27 N H -2.1986
28 K H -2.5778
29 G H -0.7785
30 A H -0.2439
31 I H 0.0000
32 I H 2.0872
33 G H 0.0000
34 L H 2.0152
35 M H 0.0000
36 V H 1.6048
37 G H 0.0000
38 G H 1.7239
39 V H 3.0414
40 V H 3.3447
9 G I 0.1841
10 Y I 1.2077
11 E I 0.6290
12 V I 0.2880
13 H I -1.1628
14 H I -1.9834
15 Q I -1.9292
16 K I -1.8564
17 L I -0.1712
18 V I 0.0000
19 F I 0.0000
20 F I 0.9132
21 A I 0.0000
22 E I -1.1430
23 D I -0.8748
24 V I 0.2980
25 G I -0.4425
26 S I -1.2125
27 N I -2.0455
28 K I 0.0000
29 G I -0.7181
30 A I 0.0000
31 I I 0.7385
32 I I 1.0200
33 G I 0.0000
34 L I 0.8967
35 M I 0.0000
36 V I 0.6695
37 G I 0.0000
38 G I 1.3831
39 V I 3.0827
40 V I 3.3993
9 G J 0.3232
10 Y J 1.3578
11 E J 0.8103
12 V J 1.0282
13 H J -0.4225
14 H J -1.7289
15 Q J -1.7943
16 K J -1.7093
17 L J 0.0672
18 V J 0.8098
19 F J 1.7105
20 F J 1.0594
21 A J 0.0000
22 E J -1.1732
23 D J -0.9769
24 V J -0.2651
25 G J -0.6751
26 S J -1.0825
27 N J -1.9930
28 K J 0.0000
29 G J 0.1020
30 A J 0.0000
31 I J 0.4822
32 I J 0.0000
33 G J 0.0000
34 L J 0.0000
35 M J 0.0000
36 V J 0.0000
37 G J 0.0000
38 G J 0.9763
39 V J 2.4584
40 V J 3.0710
9 G K 0.0774
10 Y K 1.2880
11 E K 0.6477
12 V K 0.7479
13 H K -0.6669
14 H K -1.5506
15 Q K -1.9112
16 K K -1.4751
17 L K 0.6511
18 V K 1.9116
19 F K 2.8526
20 F K 1.8538
21 A K 0.0587
22 E K -1.1144
23 D K -0.8851
24 V K 0.7729
25 G K -0.0049
26 S K -0.9617
27 N K -1.3598
28 K K -1.2196
29 G K -0.5409
30 A K 0.0000
31 I K 0.5055
32 I K 0.6700
33 G K 0.5264
34 L K 0.0000
35 M K 0.0000
36 V K 0.0000
37 G K 0.0000
38 G K 0.9355
39 V K 2.2812
40 V K 2.7073
9 G L -0.1689
10 Y L 0.8176
11 E L -0.1840
12 V L 0.8370
13 H L -0.9168
14 H L -1.7995
15 Q L -2.0409
16 K L -1.6883
17 L L 1.2973
18 V L 2.5925
19 F L 3.7106
20 F L 2.2189
21 A L 0.1569
22 E L -1.6034
23 D L -2.4774
24 V L -1.9154
25 G L -1.3997
26 S L -0.7002
27 N L -0.9458
28 K L -1.3595
29 G L -0.0809
30 A L -0.2944
31 I L 0.0994
32 I L 0.4814
33 G L 0.7023
34 L L 0.6125
35 M L 0.6795
36 V L 0.7089
37 G L 0.6787
38 G L 1.3410
39 V L 2.6068
40 V L 2.2709
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, 0.1452 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
input 0.1452 View CSV PDB
model_11 0.1176 View CSV PDB
model_2 0.1027 View CSV PDB
model_8 0.0805 View CSV PDB
model_9 0.0616 View CSV PDB
model_6 0.0595 View CSV PDB
model_1 0.0524 View CSV PDB
CABS_average 0.0502 View CSV PDB
model_3 0.0446 View CSV PDB
model_5 0.0345 View CSV PDB
model_0 0.0311 View CSV PDB
model_7 0.0288 View CSV PDB
model_10 -0.0032 View CSV PDB
model_4 -0.0073 View CSV PDB