Project name: varA_10A

Status: done

Started: 2026-03-21 17:50:32
Chain sequence(s) A: EVQLQESGGGVVQAGGSLRLSCAASGTTWNINAMGWYRQAPGKERELVARILSGGVTNYADSVKGRFTIFDINVENTLILQMNSLRPEDTAVYFCHGTTGFRDYWGQGTQVTVSS
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                                                (00:01:07)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:18:15)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:18:15)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:18:16)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:18:16)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:18:16)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:18:17)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:18:17)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:18:17)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:18:18)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:18:18)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:18:18)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:18:19)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:18:19)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:18:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:22)
Show buried residues
Minimal score value
-3.4476
Maximal score value
2.1934
Average score
-0.3779
Total score value
-43.4589
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
1 E A -1.1192
2 V A 0.6476
3 Q A -0.2433
4 L A 0.0000
5 Q A -0.9561
6 E A 0.0000
7 S A -0.9641
8 G A -1.0616
9 G A -0.8985
10 G A -0.3804
11 V A 0.7412
12 V A 0.0000
13 Q A -1.2896
14 A A -1.0172
15 G A -1.1329
16 G A -0.9423
17 S A -1.0003
18 L A -1.0849
19 R A -1.8285
20 L A 0.0000
21 S A -0.2905
22 C A 0.0000
23 A A -0.4876
24 A A 0.0000
25 S A 0.0000
26 G A -0.4809
27 T A -0.2037
28 T A 0.3564
29 W A 0.6276
30 N A -0.1223
31 I A 1.5821
32 N A 0.0000
33 A A 0.4228
34 M A 0.0000
35 G A 0.0000
36 W A 0.0000
37 Y A 0.4631
38 R A 0.0000
39 Q A -1.1589
40 A A -1.8841
41 P A -2.0441
42 G A -2.1668
43 K A -3.4446
44 E A -3.4476
45 R A -2.5699
46 E A 0.0000
47 L A 1.1920
48 V A 0.0000
49 A A 0.0000
50 R A -0.2415
51 I A 0.0000
52 L A 1.4667
53 S A 0.7276
54 G A 0.3271
55 G A 0.7534
56 V A 1.6669
57 T A 0.4170
58 N A -0.9030
59 Y A -0.5136
60 A A -0.1350
61 D A -0.2834
62 S A 0.0039
63 V A 0.7140
64 K A -0.7125
65 G A -1.4615
66 R A -2.2327
67 F A 0.0000
68 T A -0.3492
69 I A 0.0000
70 F A 2.1934
71 D A 1.6267
72 I A 1.4349
73 N A -0.1373
74 V A 1.0145
75 E A 0.0011
76 N A 0.0000
77 T A 0.7167
78 L A 0.0000
79 I A 1.1862
80 L A 0.0000
81 Q A -0.9932
82 M A 0.0000
83 N A -2.4887
84 S A -1.9435
85 L A 0.0000
86 R A -1.7529
87 P A -2.0832
88 E A -2.4278
89 D A -2.0858
90 T A -1.1544
91 A A 0.0000
92 V A -0.6542
93 Y A 0.0000
94 F A 0.0000
95 C A 0.0000
96 H A -0.5649
97 G A 0.0000
98 T A -0.1371
99 T A 0.1864
100 G A 0.3579
101 F A 0.8849
102 R A -0.9210
103 D A -1.6286
104 Y A 0.0142
105 W A 0.5442
106 G A 0.0000
107 Q A -0.8251
108 G A -1.1257
109 T A -1.4005
110 Q A -1.4561
111 V A 0.0000
112 T A -0.3584
113 V A 0.0000
114 S A -1.1501
115 S A -1.3886
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, -0.3779 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_6 -0.3779 View CSV PDB
model_5 -0.5269 View CSV PDB
model_7 -0.5417 View CSV PDB
model_8 -0.564 View CSV PDB
model_2 -0.5793 View CSV PDB
model_10 -0.5964 View CSV PDB
CABS_average -0.6115 View CSV PDB
model_9 -0.6513 View CSV PDB
model_4 -0.655 View CSV PDB
model_3 -0.6838 View CSV PDB
model_0 -0.6863 View CSV PDB
model_1 -0.6926 View CSV PDB
model_11 -0.7825 View CSV PDB
input -0.8614 View CSV PDB