Project name: ALamyloidosis

Status: done

Started: 2026-03-28 15:05:03
Chain sequence(s) A: NFMLTQPHSVSESPGKTVTISCTGSSGSIASNYVQWYQQRPGSSPTTVIYEDNQRPSGVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDSSNHVVFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
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]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:06)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:06)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:57)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:13:26)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:13:26)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:13:26)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:13:27)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:13:27)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:13:27)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:13:28)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:13:29)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:13:30)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:13:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:32)
Show buried residues
Minimal score value
-3.0085
Maximal score value
2.2756
Average score
-0.4924
Total score value
-54.6537
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 N A -0.9241
2 F A 0.4024
3 M A 1.0802
4 L A 0.0000
5 T A 0.1742
6 Q A 0.0000
7 P A -0.9270
8 H A -1.1569
9 S A -1.2578
10 V A -0.8046
11 S A -0.3969
12 E A 0.0000
13 S A -0.2294
14 P A -0.2466
15 G A -1.2268
16 K A -1.7645
17 T A -0.9087
18 V A 0.0000
19 T A -0.4171
20 I A 0.0000
21 S A -0.4874
22 C A 0.0000
23 T A -0.3605
24 G A 0.0000
25 S A -0.2472
26 S A -0.4198
27 G A -0.5747
28 S A -0.6835
29 I A 0.0000
30 A A -0.5143
31 S A -0.5609
32 N A -0.5273
33 Y A 0.0892
34 V A 0.0000
35 Q A -0.4099
36 W A 0.0000
37 Y A -0.0716
38 Q A 0.0000
39 Q A -1.1880
40 R A 0.0000
41 P A -1.3443
42 G A -1.1889
43 S A -0.5655
44 S A -0.6242
45 P A -0.5734
46 T A -0.5684
47 T A -0.4814
48 V A 0.0000
49 I A 0.0000
50 Y A -0.8364
51 E A -1.5064
52 D A -2.7709
53 N A -2.8584
54 Q A -3.0085
55 R A -2.4226
56 P A -1.6941
57 S A -1.2122
58 G A -0.4621
59 V A 0.6474
60 P A 0.0000
61 D A -2.0518
62 R A -2.6613
63 F A 0.0000
64 S A -1.3455
65 G A 0.0000
66 S A -0.5075
67 I A -0.2932
68 D A -1.1998
69 S A -0.9495
70 S A -0.8017
71 S A -0.9025
72 N A -1.0378
73 S A -0.7314
74 A A 0.0000
75 S A -0.2571
76 L A 0.0000
77 T A -0.4638
78 I A 0.0000
79 S A -0.8590
80 G A -0.4259
81 L A 0.9977
82 K A 0.0000
83 T A -0.0299
84 E A 0.0000
85 D A -1.6267
86 E A -2.6786
87 A A 0.0000
88 D A -1.7911
89 Y A 0.0000
90 Y A 0.0637
91 C A 0.0000
92 Q A 0.8273
93 S A 0.0000
94 Y A 1.3151
95 D A 0.0000
96 S A -0.4131
97 S A -0.8495
98 N A -1.2757
99 H A -0.6542
100 V A 1.3318
101 V A 0.0000
102 F A 2.2756
103 G A 0.6509
104 G A 0.1115
105 G A -0.6923
106 T A 0.0000
107 K A -2.4471
108 L A 0.0000
109 T A -0.8384
110 V A 0.3502
111 L A 1.2367
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, -0.4924 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 -0.4924 View CSV PDB
model_4 -0.5204 View CSV PDB
model_6 -0.5286 View CSV PDB
model_8 -0.53 View CSV PDB
model_9 -0.534 View CSV PDB
model_2 -0.5611 View CSV PDB
model_3 -0.5667 View CSV PDB
CABS_average -0.5803 View CSV PDB
model_5 -0.59 View CSV PDB
model_10 -0.6013 View CSV PDB
model_11 -0.6114 View CSV PDB
input -0.63 View CSV PDB
model_7 -0.701 View CSV PDB
model_0 -0.7265 View CSV PDB