Project name: L41A

Status: done

Started: 2026-03-04 14:45:19
Chain sequence(s) A: MDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDAT
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]                                                (00:00:03)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:03)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:03)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:03)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:05:33)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:38:12)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:38:12)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:38:13)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:38:14)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:38:15)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:38:16)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:38:17)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:38:18)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:38:18)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:38:19)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:38:20)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:38:21)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:38:22)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:38:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:38:27)
Show buried residues
Minimal score value
-3.7709
Maximal score value
0.0
Average score
-1.2664
Total score value
-234.2929
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 M A -1.3479
2 D A -2.4640
3 V A -1.8115
4 D A -3.0849
5 E A -3.2772
6 M A 0.0000
7 L A -2.3892
8 K A -2.9245
9 Q A -2.4186
10 V A 0.0000
11 E A -2.6609
12 I A -1.7686
13 L A 0.0000
14 R A -2.4815
15 R A -2.2050
16 L A -0.8685
17 G A -1.5698
18 A A 0.0000
19 K A -1.9611
20 Q A -1.3218
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -1.1830
25 S A -1.3505
26 D A -2.5436
27 D A -1.7533
28 W A -1.3148
29 R A -2.0202
30 I A -1.1495
31 L A 0.0000
32 Q A -1.6209
33 E A -2.0002
34 A A 0.0000
35 L A 0.0000
36 K A -2.8323
37 K A -2.8078
38 G A -2.2598
39 G A 0.0000
40 D A -1.4956
41 I A 0.0000
42 A A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A 0.0000
46 A A 0.0000
47 T A -1.5459
48 D A -2.3199
49 V A -1.0972
50 D A -2.6225
51 E A -3.1112
52 M A 0.0000
53 L A -2.2871
54 K A -2.5599
55 Q A 0.0000
56 V A 0.0000
57 E A -2.5617
58 I A -1.6689
59 L A 0.0000
60 R A -2.3394
61 R A -2.1603
62 L A -0.7198
63 G A -1.5477
64 A A 0.0000
65 K A -2.3168
66 Q A -1.5431
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -1.1383
71 S A -1.3039
72 D A -2.4236
73 D A -1.6947
74 W A -1.2419
75 R A -2.1566
76 I A -1.5078
77 L A 0.0000
78 Q A -1.6436
79 E A -2.3998
80 A A 0.0000
81 L A 0.0000
82 K A -2.7296
83 K A -2.6815
84 G A -2.0524
85 G A 0.0000
86 D A -1.6017
87 I A 0.0000
88 A A 0.0000
89 I A 0.0000
90 V A 0.0000
91 D A -1.5649
92 A A -1.8533
93 T A -1.5625
94 D A -2.5115
95 V A -1.5756
96 D A -2.9008
97 E A -3.0958
98 M A 0.0000
99 L A -2.0800
100 K A -2.1936
101 Q A 0.0000
102 V A 0.0000
103 E A -1.9990
104 I A -1.2797
105 L A 0.0000
106 R A -2.0916
107 R A -1.9034
108 L A -0.4614
109 G A -1.2978
110 A A -1.6523
111 K A -2.0784
112 Q A -1.4868
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -1.1488
117 S A 0.0000
118 D A -2.8646
119 D A -1.6535
120 W A -1.4717
121 R A -2.1041
122 I A -1.0875
123 L A 0.0000
124 Q A -1.7152
125 E A -2.5800
126 A A 0.0000
127 L A -1.7912
128 K A -2.7202
129 K A -2.5779
130 G A -1.8552
131 G A -1.3429
132 D A 0.0000
133 I A 0.0000
134 A A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -2.7295
138 A A -2.7150
139 T A -1.9730
140 D A -2.6292
141 V A -1.3647
142 D A -3.0297
143 E A -3.7709
144 M A 0.0000
145 L A -2.4172
146 K A -2.7573
147 Q A 0.0000
148 V A 0.0000
149 E A -2.5765
150 I A -1.7189
151 L A 0.0000
152 R A -2.4095
153 R A -2.3683
154 L A -1.2882
155 G A -1.6627
156 A A 0.0000
157 K A -1.8885
158 Q A -1.1374
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -1.0535
163 S A 0.0000
164 D A -1.6762
165 D A -1.3480
166 W A -1.2094
167 R A -1.9926
168 I A -1.0615
169 L A 0.0000
170 Q A -1.5419
171 E A -2.0729
172 A A 0.0000
173 L A -1.5885
174 K A -2.4472
175 K A -2.6810
176 G A -1.9249
177 G A -1.3860
178 D A 0.0000
179 I A 0.0000
180 A A 0.0000
181 I A 0.0000
182 V A 0.0000
183 D A 0.0000
184 A A -1.0102
185 T A -0.4981
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, -1.2664 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
input -1.2664 View CSV PDB
model_1 -1.3094 View CSV PDB
model_11 -1.3113 View CSV PDB
model_7 -1.3176 View CSV PDB
model_3 -1.3262 View CSV PDB
model_9 -1.3289 View CSV PDB
model_2 -1.333 View CSV PDB
model_8 -1.3339 View CSV PDB
CABS_average -1.3557 View CSV PDB
model_4 -1.3663 View CSV PDB
model_6 -1.3859 View CSV PDB
model_0 -1.3935 View CSV PDB
model_10 -1.3941 View CSV PDB
model_5 -1.4681 View CSV PDB