Project name: varB_5A

Status: done

Started: 2026-03-21 17:51:15
Chain sequence(s) A: EVQLVESGGGVVQPGGSLRLSCAASGTTWNINAMGWYRQAPGKERELVARILSGGVTYYADSVKGRFTISDINSKNTLYLQMNSLRPEDTAVYYCHGTTGFRDYWGQGTLVTVSS
input PDB
Selected Chain(s) A
Distance of aggregation 5 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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[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                                                (00:01:00)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:18:31)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:18:33)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:18:33)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:18:33)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:18:34)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:18:34)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:18:34)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:18:35)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:18:35)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:18:35)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:18:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:38)
Show buried residues
Minimal score value
-2.2928
Maximal score value
1.7497
Average score
-0.1372
Total score value
-15.7818
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 -0.0508
2 V A 1.5088
3 Q A -0.4975
4 L A 0.0000
5 V A 1.5412
6 E A 0.0343
7 S A -0.2047
8 G A -0.4676
9 G A -0.4324
10 G A 0.1209
11 V A 1.7497
12 V A 0.0000
13 Q A -0.8193
14 P A -0.4957
15 G A -0.5486
16 G A -0.3131
17 S A -0.3203
18 L A 0.0000
19 R A -1.8445
20 L A 0.0000
21 S A 0.0000
22 C A 0.0000
23 A A 0.0213
24 A A 0.0000
25 S A -0.2439
26 G A 0.0206
27 T A -0.1157
28 T A -0.0543
29 W A -0.1084
30 N A -1.2442
31 I A 0.0000
32 N A -0.2527
33 A A 0.0670
34 M A 0.0000
35 G A 0.0000
36 W A 0.0000
37 Y A 0.2411
38 R A 0.0000
39 Q A -0.7468
40 A A 0.0000
41 P A -0.4278
42 G A -0.6464
43 K A -1.1605
44 E A -2.2928
45 R A -2.2913
46 E A -0.3976
47 L A 0.9116
48 V A 0.0000
49 A A 0.0000
50 R A -0.4333
51 I A 0.0000
52 L A 0.7263
53 S A -0.1538
54 G A -0.5950
55 G A -0.4332
56 V A 0.5539
57 T A 0.3469
58 Y A 1.5221
59 Y A 1.5599
60 A A -0.0816
61 D A -1.7977
62 S A -0.3099
63 V A 0.3628
64 K A -0.2402
65 G A 0.0000
66 R A -1.8441
67 F A 0.0000
68 T A 0.0248
69 I A 0.3983
70 S A -0.0547
71 D A -0.0748
72 I A 1.3877
73 N A -0.4799
74 S A -0.6359
75 K A -1.7998
76 N A 0.0000
77 T A -0.0072
78 L A 0.0000
79 Y A 0.3651
80 L A 0.0000
81 Q A -0.6608
82 M A 0.0000
83 N A -0.6706
84 S A -0.1174
85 L A 0.3294
86 R A 0.0000
87 P A -0.2302
88 E A -0.7703
89 D A -1.8686
90 T A -0.4037
91 A A 0.0000
92 V A 0.4607
93 Y A 0.0000
94 Y A 0.0000
95 C A 0.0000
96 H A -0.1425
97 G A 0.0000
98 T A -0.1644
99 T A -0.1956
100 G A -0.0973
101 F A 1.6809
102 R A -0.7251
103 D A -1.1811
104 Y A 0.1858
105 W A 1.2060
106 G A -0.0620
107 Q A -1.2772
108 G A -0.5912
109 T A 0.0000
110 L A 1.1096
111 V A 0.0000
112 T A 0.2075
113 V A 0.1241
114 S A -0.2207
115 S A -0.2534
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, -0.1372 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_5 -0.1372 View CSV PDB
model_10 -0.1692 View CSV PDB
model_11 -0.1907 View CSV PDB
model_3 -0.196 View CSV PDB
model_9 -0.2183 View CSV PDB
CABS_average -0.2189 View CSV PDB
model_0 -0.2201 View CSV PDB
model_4 -0.2208 View CSV PDB
model_7 -0.2241 View CSV PDB
model_1 -0.245 View CSV PDB
model_6 -0.251 View CSV PDB
model_2 -0.2563 View CSV PDB
input -0.2728 View CSV PDB
model_8 -0.2985 View CSV PDB