Project name: Trail1

Status: done

Started: 2026-07-17 11:09:40
Chain sequence(s) A: NNEESPTATVAEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
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                                                (00:01:47)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:19:13)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:19:13)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:19:14)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:19:14)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:19:14)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:19:15)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:19:16)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:19:16)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:19:16)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:19:17)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:19:17)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:19:18)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:19:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:22)
Show buried residues
Minimal score value
-2.4829
Maximal score value
1.5107
Average score
-0.4287
Total score value
-56.582
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 N A -1.5161
10 N A -1.8566
11 E A -2.1656
12 E A -0.9479
13 S A -0.3141
14 P A 0.0000
15 T A -0.0065
16 A A 0.0507
17 T A -0.0130
18 V A 0.0000
19 A A -0.2817
20 E A -2.0345
21 Q A -1.5748
22 G A -0.6356
23 E A -1.5741
24 D A -1.9442
25 I A -0.1262
26 T A -0.0752
27 S A -0.3840
28 K A -1.1696
29 K A -1.9678
30 D A -1.2738
31 R A -1.9769
32 G A -0.4532
33 V A 0.0000
34 L A -0.1489
35 K A -0.2012
36 I A 0.0000
37 V A 0.0666
38 K A -1.8013
39 R A -0.9020
40 V A 1.5107
41 G A -0.1512
42 N A -0.3028
43 G A -0.8321
44 E A -2.2563
45 E A -2.1710
46 T A -0.4119
47 P A -0.1824
48 M A 0.5078
49 I A 0.9189
50 G A -0.0581
51 D A -1.4510
52 K A -0.9073
53 V A 0.0000
54 Y A 0.3992
55 V A 0.0000
56 H A -0.2892
57 Y A 0.0000
58 K A -0.2228
59 G A 0.0000
60 K A 0.0000
61 L A 0.0000
62 S A -0.2797
63 N A -1.2763
64 G A -0.6829
65 K A -1.6140
66 K A -0.7963
67 F A 0.2579
68 D A -0.6605
69 S A 0.0000
70 S A -0.3315
71 H A -1.1494
72 D A -2.2475
73 R A -2.4829
74 N A -1.7213
75 E A -0.8001
76 P A -0.0972
77 F A 0.4967
78 V A 0.6659
79 F A 0.0000
80 S A 0.0660
81 L A 1.1308
82 G A -0.2808
83 K A -0.3943
84 G A -0.6503
85 Q A -1.2399
86 V A -0.0640
87 I A 0.0000
88 K A -0.7122
89 A A 0.0000
90 W A 0.0000
91 D A -0.7008
92 I A 0.3122
93 G A 0.0000
94 V A 0.0000
95 A A 0.0835
96 T A 0.0000
97 M A 0.0000
98 K A 0.0000
99 K A -1.7196
100 G A -0.4253
101 E A 0.0000
102 I A 0.4350
103 C A 0.0000
104 H A 0.0000
105 L A 0.0000
106 L A 0.0000
107 C A 0.0000
108 K A -0.2655
109 P A -0.3603
110 E A -0.5842
111 Y A 0.0000
112 A A 0.0000
113 Y A 0.0641
114 G A -0.4622
115 S A -0.1912
116 A A -0.0667
117 G A -0.4569
118 S A 0.0000
119 L A 0.0000
120 P A 0.0000
121 K A -0.4989
122 I A 1.3856
123 P A 0.2222
124 S A -0.3993
125 N A -1.2904
126 A A -0.1890
127 T A -0.0194
128 L A 0.0000
129 F A 0.0000
130 F A 0.0000
131 E A -0.6623
132 I A 0.0000
133 E A -0.9439
134 L A 0.0000
135 L A 0.4681
136 D A -1.3036
137 F A 1.1002
138 K A -1.1911
139 G A -1.0330
140 E A -1.8985
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, -0.4287 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_0 -0.4287 View CSV PDB
model_10 -0.4441 View CSV PDB
model_6 -0.4555 View CSV PDB
model_11 -0.4583 View CSV PDB
input -0.4616 View CSV PDB
model_2 -0.4764 View CSV PDB
CABS_average -0.482 View CSV PDB
model_4 -0.4867 View CSV PDB
model_3 -0.4881 View CSV PDB
model_9 -0.5024 View CSV PDB
model_5 -0.5052 View CSV PDB
model_7 -0.5085 View CSV PDB
model_8 -0.5135 View CSV PDB
model_1 -0.5164 View CSV PDB