Project name: I40L_X2

Status: done

Started: 2026-02-27 20:54:29
Chain sequence(s) A: MDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDLLIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDLLIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDAT
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:06:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:48:18)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:48:19)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:48:20)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:48:21)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:48:22)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:48:23)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:48:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:48:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:48:27)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:48:28)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:48:29)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:48:30)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:48:31)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:48:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:48:40)
Show buried residues
Minimal score value
-3.1755
Maximal score value
0.0
Average score
-1.1711
Total score value
-216.6623
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 -1.3418
2 D A -2.4099
3 V A -1.4096
4 D A -2.5421
5 E A -3.0823
6 M A 0.0000
7 L A -2.0887
8 K A -2.4625
9 Q A 0.0000
10 V A 0.0000
11 E A -1.9545
12 I A -1.2284
13 L A 0.0000
14 R A -2.0820
15 R A -1.9863
16 L A -0.8132
17 G A -1.3094
18 A A 0.0000
19 K A -1.8955
20 Q A -1.1837
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -0.4927
25 S A 0.0000
26 D A -1.7030
27 D A -1.4496
28 W A -1.4130
29 R A -2.1120
30 I A -1.1641
31 L A 0.0000
32 Q A -1.7793
33 E A -1.8994
34 A A 0.0000
35 L A -1.6934
36 K A -2.3420
37 K A -2.2583
38 G A -1.4349
39 G A 0.0000
40 D A -1.2731
41 L A 0.0000
42 L A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A 0.0000
46 A A -1.3449
47 T A -1.3616
48 D A -2.3040
49 V A -1.6600
50 D A -2.9226
51 E A -2.8790
52 M A 0.0000
53 L A -2.4468
54 K A -2.7652
55 Q A 0.0000
56 V A 0.0000
57 E A -2.7604
58 I A -1.8128
59 L A 0.0000
60 R A -2.3953
61 R A -2.2924
62 L A -1.4068
63 G A -1.6971
64 A A 0.0000
65 K A -1.9755
66 Q A -1.2328
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -0.8603
71 S A 0.0000
72 D A -2.5241
73 D A -1.8623
74 W A -1.5856
75 R A -2.1587
76 I A -1.5345
77 L A 0.0000
78 Q A -1.6511
79 E A -2.1410
80 A A 0.0000
81 L A -1.8112
82 K A -2.6300
83 K A -2.7365
84 G A -1.8878
85 G A 0.0000
86 D A 0.0000
87 I A 0.0000
88 L A 0.0000
89 I A 0.0000
90 V A 0.0000
91 D A 0.0000
92 A A -1.4998
93 T A -1.4877
94 D A -2.4508
95 V A -1.9560
96 D A -3.0255
97 E A -3.1755
98 M A 0.0000
99 L A -2.4539
100 K A -2.6938
101 Q A 0.0000
102 V A 0.0000
103 E A -2.5144
104 I A -1.6261
105 L A 0.0000
106 R A -2.3178
107 R A -2.2216
108 L A -1.1228
109 G A -1.4781
110 A A 0.0000
111 K A -1.9202
112 Q A -1.1390
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -0.8881
117 S A 0.0000
118 D A -2.4558
119 D A -1.8793
120 W A -1.6454
121 R A -2.1079
122 I A -1.5556
123 L A 0.0000
124 Q A -1.6695
125 E A -2.1250
126 A A 0.0000
127 L A -1.7506
128 K A -2.5835
129 K A -2.5906
130 G A -1.7885
131 G A 0.0000
132 D A 0.0000
133 L A 0.0000
134 L A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.3323
138 A A -1.6334
139 T A -1.5743
140 D A -1.9894
141 V A -1.6965
142 D A -2.8361
143 E A -3.1090
144 M A 0.0000
145 L A -2.2814
146 K A -2.7026
147 Q A 0.0000
148 V A 0.0000
149 E A -2.3734
150 I A -1.5973
151 L A 0.0000
152 R A -2.2142
153 R A -2.1766
154 L A -1.3443
155 G A -1.6450
156 A A 0.0000
157 K A -1.9480
158 Q A -1.1848
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -1.1779
163 S A 0.0000
164 D A -2.5674
165 D A -2.0084
166 W A -1.6059
167 R A -2.1188
168 I A -1.4966
169 L A 0.0000
170 Q A -1.1594
171 E A -1.4562
172 A A 0.0000
173 L A -1.2932
174 K A -2.2325
175 K A -2.1966
176 G A -1.5477
177 G A 0.0000
178 D A 0.0000
179 I A 0.0000
180 L A 0.0000
181 I A 0.0000
182 V A 0.0000
183 D A 0.0000
184 A A 0.0000
185 T A -0.5953
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, -1.1711 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 -1.1711 View CSV PDB
model_4 -1.2376 View CSV PDB
model_2 -1.2533 View CSV PDB
model_9 -1.2941 View CSV PDB
model_7 -1.3325 View CSV PDB
model_1 -1.3382 View CSV PDB
model_8 -1.3534 View CSV PDB
CABS_average -1.3542 View CSV PDB
model_0 -1.3658 View CSV PDB
model_3 -1.3706 View CSV PDB
model_6 -1.3709 View CSV PDB
model_11 -1.3759 View CSV PDB
model_5 -1.4514 View CSV PDB
model_10 -1.507 View CSV PDB