Project name: L41A_X2

Status: done

Started: 2026-02-27 20:58:07
Chain sequence(s) A: MDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDIAIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDAT
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                                                (00:05:54)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:50:43)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:50:44)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:50:45)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:50:46)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:50:47)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:50:48)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:50:49)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:50:50)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:50:51)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:50:52)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:50:53)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:50:53)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:50:54)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:50:59)
[INFO]       Main:     Simulation completed successfully.                                          (00:51:00)
Show buried residues
Minimal score value
-3.2097
Maximal score value
0.0
Average score
-1.1918
Total score value
-220.4887
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 -1.1199
2 D A -2.2321
3 V A -1.7000
4 D A -2.9234
5 E A -2.8577
6 M A 0.0000
7 L A -2.3508
8 K A -2.5025
9 Q A 0.0000
10 V A 0.0000
11 E A -2.4159
12 I A -1.5485
13 L A 0.0000
14 R A -2.2304
15 R A -2.1779
16 L A -1.2334
17 G A -1.6165
18 A A 0.0000
19 K A -1.9320
20 Q A -1.1638
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -0.6914
25 S A 0.0000
26 D A -2.2857
27 D A -1.7202
28 W A -1.4920
29 R A -2.1762
30 I A -1.3959
31 L A 0.0000
32 Q A -1.6928
33 E A -2.2834
34 A A 0.0000
35 L A -1.7579
36 K A -2.4933
37 K A -2.4879
38 G A -1.7054
39 G A -1.3610
40 D A 0.0000
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 -1.4200
47 T A -1.4462
48 D A -2.3378
49 V A -1.5351
50 D A -2.8169
51 E A -2.9813
52 M A 0.0000
53 L A -2.3662
54 K A -2.7004
55 Q A 0.0000
56 V A 0.0000
57 E A -2.5907
58 I A -1.6121
59 L A 0.0000
60 R A -2.3230
61 R A -2.1724
62 L A -1.1675
63 G A -1.4411
64 A A 0.0000
65 K A -1.9153
66 Q A -1.1755
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -0.8357
71 S A 0.0000
72 D A -2.5067
73 D A -1.8283
74 W A -1.5904
75 R A -2.1101
76 I A -1.4380
77 L A 0.0000
78 Q A -1.5546
79 E A -1.8441
80 A A 0.0000
81 L A -1.7613
82 K A -2.6547
83 K A -2.7454
84 G A -1.8494
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 -1.4086
93 T A -1.4437
94 D A -2.3633
95 V A -1.4911
96 D A -2.8220
97 E A -2.9309
98 M A 0.0000
99 L A -2.1758
100 K A -2.3944
101 Q A 0.0000
102 V A 0.0000
103 E A -2.2716
104 I A -1.3970
105 L A 0.0000
106 R A -2.2983
107 R A -2.0757
108 L A -0.9165
109 G A -1.5496
110 A A 0.0000
111 K A -1.9098
112 Q A -1.1487
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -0.8125
117 S A 0.0000
118 D A -2.4350
119 D A -1.8953
120 W A -1.6212
121 R A -2.1591
122 I A -1.4201
123 L A 0.0000
124 Q A -1.5122
125 E A -1.9167
126 A A 0.0000
127 L A -1.4707
128 K A -2.4543
129 K A -2.3841
130 G A -1.6983
131 G A -1.3227
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 -1.5178
138 A A 0.0000
139 T A -1.6923
140 D A -2.0923
141 V A -1.6740
142 D A -2.8974
143 E A -3.2097
144 M A 0.0000
145 L A -2.4256
146 K A -2.8708
147 Q A 0.0000
148 V A 0.0000
149 E A -2.9057
150 I A -1.9293
151 L A 0.0000
152 R A -2.6028
153 R A -2.4224
154 L A -1.2399
155 G A -1.5403
156 A A 0.0000
157 K A -1.9564
158 Q A -1.1755
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -0.8688
163 S A 0.0000
164 D A -2.2856
165 D A -1.8899
166 W A -1.6003
167 R A -2.0724
168 I A -1.4855
169 L A 0.0000
170 Q A -1.5856
171 E A -1.9076
172 A A 0.0000
173 L A -1.7676
174 K A -2.4346
175 K A -2.8055
176 G A -1.9082
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 -1.0839
184 A A 0.0000
185 T A -0.6737
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, -1.1918 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 -1.1918 View CSV PDB
model_5 -1.2622 View CSV PDB
model_9 -1.278 View CSV PDB
model_2 -1.2823 View CSV PDB
model_7 -1.3396 View CSV PDB
CABS_average -1.3551 View CSV PDB
model_8 -1.3556 View CSV PDB
model_4 -1.3623 View CSV PDB
model_10 -1.376 View CSV PDB
model_11 -1.3795 View CSV PDB
model_6 -1.386 View CSV PDB
model_1 -1.392 View CSV PDB
model_3 -1.3962 View CSV PDB
model_0 -1.4513 View CSV PDB