Project name: L41S_X2

Status: done

Started: 2026-02-27 20:59:17
Chain sequence(s) A: MDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDISIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDISIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDAT
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                                          (00:00:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:06:30)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:49:28)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:49:29)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:49:30)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:49:31)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:49:32)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:49:33)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:49:34)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:49:35)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:49:36)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:49:37)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:49:38)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:49:39)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:49:40)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:49:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:49:46)
Show buried residues
Minimal score value
-3.3594
Maximal score value
0.0
Average score
-1.2089
Total score value
-223.6385
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 -1.3342
2 D A -2.6068
3 V A -2.1176
4 D A -3.2256
5 E A -3.3594
6 M A 0.0000
7 L A 0.0000
8 K A -2.9525
9 Q A 0.0000
10 V A 0.0000
11 E A -2.0028
12 I A -1.2644
13 L A 0.0000
14 R A -2.1694
15 R A -2.0363
16 L A -1.0164
17 G A -1.3995
18 A A 0.0000
19 K A -1.9110
20 Q A -1.1797
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -0.9652
25 S A 0.0000
26 D A -2.5818
27 D A -1.8679
28 W A -1.6140
29 R A -2.0997
30 I A -1.6010
31 L A 0.0000
32 Q A -1.6507
33 E A -2.2079
34 A A 0.0000
35 L A -1.8845
36 K A -2.6110
37 K A -2.8189
38 G A -1.8786
39 G A -1.4463
40 D A 0.0000
41 I A 0.0000
42 S A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A -1.3257
46 A A -1.5818
47 T A -1.5881
48 D A -2.5185
49 V A -1.7152
50 D A -3.0109
51 E A -3.2008
52 M A 0.0000
53 L A -2.3903
54 K A -2.7493
55 Q A 0.0000
56 V A 0.0000
57 E A -2.6031
58 I A -1.7036
59 L A 0.0000
60 R A -2.3748
61 R A -2.2461
62 L A -1.3113
63 G A -1.7860
64 A A 0.0000
65 K A -1.9441
66 Q A -1.1777
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -0.8798
71 S A 0.0000
72 D A -2.4138
73 D A -1.8877
74 W A -1.5020
75 R A -2.1171
76 I A -1.4803
77 L A 0.0000
78 Q A -1.5525
79 E A -2.0208
80 A A 0.0000
81 L A -1.7106
82 K A -2.4973
83 K A -2.5349
84 G A -1.7516
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 -1.4538
92 A A -1.6233
93 T A -1.6525
94 D A -2.1324
95 V A -1.8321
96 D A -2.9467
97 E A -3.2255
98 M A 0.0000
99 L A -2.2415
100 K A -2.3498
101 Q A 0.0000
102 V A 0.0000
103 E A -1.7860
104 I A -1.1040
105 L A 0.0000
106 R A -2.1089
107 R A -2.0098
108 L A -1.1291
109 G A -1.5832
110 A A 0.0000
111 K A -1.9229
112 Q A -1.1612
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -0.9695
117 S A 0.0000
118 D A -2.4535
119 D A -1.9255
120 W A -1.6012
121 R A -2.0292
122 I A -1.5084
123 L A 0.0000
124 Q A -1.4994
125 E A -1.8520
126 A A 0.0000
127 L A -1.6921
128 K A -2.6236
129 K A -2.8188
130 G A -1.7040
131 G A -1.4125
132 D A 0.0000
133 I A 0.0000
134 S A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.4757
138 A A 0.0000
139 T A -1.6676
140 D A -2.1250
141 V A -1.8150
142 D A -2.9343
143 E A -3.1881
144 M A 0.0000
145 L A -2.3602
146 K A -2.7092
147 Q A 0.0000
148 V A 0.0000
149 E A -2.5177
150 I A -1.7510
151 L A 0.0000
152 R A -2.3912
153 R A -2.3499
154 L A -1.6495
155 G A -1.8209
156 A A 0.0000
157 K A -1.9743
158 Q A -1.2066
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -0.8242
163 S A 0.0000
164 D A -2.3378
165 D A -1.7067
166 W A -1.4295
167 R A -1.9872
168 I A -1.4254
169 L A 0.0000
170 Q A -1.2007
171 E A -1.4279
172 A A 0.0000
173 L A -1.2409
174 K A -2.2414
175 K A -2.2088
176 G A -1.5615
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 -1.3529
184 A A 0.0000
185 T A -1.0262
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, -1.2089 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 -1.2089 View CSV PDB
model_11 -1.3046 View CSV PDB
model_1 -1.3213 View CSV PDB
model_2 -1.3265 View CSV PDB
model_9 -1.3288 View CSV PDB
model_5 -1.3291 View CSV PDB
model_7 -1.341 View CSV PDB
model_3 -1.355 View CSV PDB
CABS_average -1.3672 View CSV PDB
model_6 -1.389 View CSV PDB
model_8 -1.4036 View CSV PDB
model_0 -1.4236 View CSV PDB
model_10 -1.4242 View CSV PDB
model_4 -1.4597 View CSV PDB