Project name: varA

Status: done

Started: 2026-03-21 17:49:27
Chain sequence(s) A: EVQLQESGGGVVQAGGSLRLSCAASGTTWNINAMGWYRQAPGKERELVARILSGGVTNYADSVKGRFTIFDINVENTLILQMNSLRPEDTAVYFCHGTTGFRDYWGQGTQVTVSS
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]                                                (00:00:01)
[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                                                (00:01:04)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:18:28)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:18:28)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:18:29)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:18:29)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:18:29)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:18:30)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:18:30)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:18:30)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:18:31)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:18:31)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:18:32)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:18:35)
[INFO]       Main:     Simulation completed successfully.                                          (00:18:36)
Show buried residues
Minimal score value
-2.3149
Maximal score value
1.8706
Average score
-0.1923
Total score value
-22.1167
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 -1.4795
2 V A 1.2870
3 Q A -0.4590
4 L A 0.0000
5 Q A -1.1983
6 E A 0.0000
7 S A -0.2249
8 G A -0.1938
9 G A -0.4919
10 G A 0.1835
11 V A 1.7598
12 V A 0.0000
13 Q A -0.8171
14 A A -0.1885
15 G A -0.4761
16 G A -0.2406
17 S A -0.2222
18 L A -0.2391
19 R A -1.8497
20 L A 0.0000
21 S A -0.0031
22 C A 0.0000
23 A A 0.0165
24 A A 0.0027
25 S A -0.1285
26 G A -0.4820
27 T A -0.1503
28 T A -0.0679
29 W A 0.0000
30 N A -0.4247
31 I A 1.8555
32 N A 0.0000
33 A A 0.1790
34 M A 0.0000
35 G A -0.2235
36 W A 0.0000
37 Y A 0.4048
38 R A 0.0000
39 Q A -0.5662
40 A A 0.0000
41 P A -0.4307
42 G A -0.6626
43 K A -1.2435
44 E A -2.3149
45 R A -2.2940
46 E A -0.6511
47 L A 0.1899
48 V A 0.0000
49 A A 0.0000
50 R A -1.3128
51 I A 0.0000
52 L A 1.2974
53 S A 0.0834
54 G A -0.5005
55 G A 0.2250
56 V A 1.2018
57 T A 0.0773
58 N A -0.2535
59 Y A 1.2289
60 A A -0.0562
61 D A -1.7908
62 S A -0.3393
63 V A -0.1214
64 K A -1.7258
65 G A -1.0531
66 R A -1.9128
67 F A 0.0000
68 T A -0.0475
69 I A 0.0000
70 F A 1.8706
71 D A 0.0920
72 I A 0.1109
73 N A -0.8657
74 V A 1.1962
75 E A -1.4869
76 N A 0.0000
77 T A 0.0000
78 L A 0.0000
79 I A 0.6165
80 L A 0.0000
81 Q A -0.5598
82 M A 0.0000
83 N A -0.2438
84 S A 0.0000
85 L A 0.0000
86 R A -1.6345
87 P A -0.9065
88 E A -1.8685
89 D A 0.0000
90 T A -0.0743
91 A A 0.0000
92 V A 0.0809
93 Y A 0.0000
94 F A 0.1809
95 C A 0.0000
96 H A -0.0798
97 G A 0.0000
98 T A -0.1827
99 T A 0.0000
100 G A -0.0996
101 F A 1.7224
102 R A -0.4865
103 D A -1.1087
104 Y A 0.3672
105 W A 1.1709
106 G A -0.0594
107 Q A -1.2303
108 G A -0.4954
109 T A 0.0000
110 Q A -1.1693
111 V A 0.0000
112 T A 0.0137
113 V A 0.2499
114 S A -0.1663
115 S A -0.2259
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, -0.1923 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_1 -0.1923 View CSV PDB
model_10 -0.2148 View CSV PDB
model_7 -0.2291 View CSV PDB
model_0 -0.2362 View CSV PDB
model_3 -0.2473 View CSV PDB
CABS_average -0.2503 View CSV PDB
model_5 -0.2534 View CSV PDB
model_2 -0.2551 View CSV PDB
model_4 -0.259 View CSV PDB
model_9 -0.26 View CSV PDB
model_8 -0.2789 View CSV PDB
model_6 -0.2807 View CSV PDB
model_11 -0.2973 View CSV PDB
input -0.3289 View CSV PDB