Project name: L41A

Status: done

Started: 2026-02-27 20:57:27
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                                                (00:06:36)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:47:32)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:47:33)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:47:34)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:47:35)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:47:36)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:47:37)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:47:38)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:47:39)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:47:40)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:47:41)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:47:42)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:47:43)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:47:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:47:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:47:51)
Show buried residues
Minimal score value
-3.1448
Maximal score value
0.0
Average score
-1.2429
Total score value
-229.9453
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 -1.2323
2 D A -2.3635
3 V A -1.8033
4 D A -3.0926
5 E A -3.1448
6 M A 0.0000
7 L A -2.5728
8 K A -2.7320
9 Q A 0.0000
10 V A 0.0000
11 E A -2.2580
12 I A -1.3816
13 L A 0.0000
14 R A -2.0721
15 R A -1.8145
16 L A -0.4440
17 G A -1.2076
18 A A 0.0000
19 K A -1.8280
20 Q A -1.1403
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -1.0449
25 S A 0.0000
26 D A -2.7232
27 D A -1.8770
28 W A -1.7032
29 R A -2.3075
30 I A -1.6364
31 L A 0.0000
32 Q A -1.8052
33 E A -2.7327
34 A A 0.0000
35 L A -2.0951
36 K A -2.6747
37 K A -2.5491
38 G A -1.7565
39 G A -1.5562
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 -1.6214
46 A A -2.0194
47 T A -1.6683
48 D A -2.6435
49 V A -1.6819
50 D A -2.8886
51 E A -3.1062
52 M A 0.0000
53 L A -2.4925
54 K A -2.8827
55 Q A 0.0000
56 V A 0.0000
57 E A -3.0140
58 I A -1.7724
59 L A 0.0000
60 R A -2.5323
61 R A -2.3000
62 L A -1.1820
63 G A -1.5793
64 A A 0.0000
65 K A -1.9065
66 Q A -1.1513
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -1.4889
71 S A -1.5397
72 D A -2.6926
73 D A -1.8540
74 W A -1.6699
75 R A -2.0545
76 I A -1.2347
77 L A 0.0000
78 Q A -1.4029
79 E A -1.8582
80 A A 0.0000
81 L A -1.8488
82 K A -2.5544
83 K A -2.6195
84 G A -1.8476
85 G A -1.4316
86 D A 0.0000
87 I A 0.0000
88 A A 0.0000
89 I A 0.0000
90 V A 0.0000
91 D A -1.5723
92 A A -2.0905
93 T A -1.5808
94 D A -2.5274
95 V A -1.5800
96 D A -2.8617
97 E A -2.9791
98 M A 0.0000
99 L A -2.2195
100 K A -2.4808
101 Q A 0.0000
102 V A 0.0000
103 E A -2.0919
104 I A -1.3154
105 L A 0.0000
106 R A -2.1059
107 R A -1.9093
108 L A -0.6658
109 G A -1.2242
110 A A 0.0000
111 K A -1.8512
112 Q A -1.1378
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A 0.0000
117 S A -1.1652
118 D A -2.5268
119 D A -1.7642
120 W A -1.5336
121 R A -2.0302
122 I A -1.2422
123 L A 0.0000
124 Q A -1.3498
125 E A -1.8619
126 A A 0.0000
127 L A -1.4948
128 K A -2.3817
129 K A -2.2754
130 G A -1.6008
131 G A -1.2537
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 -1.3895
138 A A -1.9133
139 T A -1.6318
140 D A -2.5507
141 V A -1.5532
142 D A -2.7625
143 E A -2.9198
144 M A 0.0000
145 L A -2.1045
146 K A -2.3163
147 Q A 0.0000
148 V A 0.0000
149 E A -1.8317
150 I A -1.1245
151 L A 0.0000
152 R A -2.0457
153 R A -1.8267
154 L A -0.5981
155 G A -1.2054
156 A A 0.0000
157 K A -1.8615
158 Q A -1.1342
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -1.2040
163 S A -1.4760
164 D A -2.5103
165 D A -1.8151
166 W A -1.5032
167 R A -2.0734
168 I A -1.2201
169 L A 0.0000
170 Q A -1.3461
171 E A -1.7381
172 A A 0.0000
173 L A -1.8046
174 K A -2.3843
175 K A -2.2237
176 G A -1.5722
177 G A -1.4175
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 -1.2012
184 A A 0.0000
185 T A -0.9235
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, -1.2429 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 -1.2429 View CSV PDB
model_1 -1.2468 View CSV PDB
model_3 -1.3191 View CSV PDB
model_6 -1.3199 View CSV PDB
model_2 -1.3364 View CSV PDB
model_7 -1.3744 View CSV PDB
CABS_average -1.3746 View CSV PDB
model_0 -1.3804 View CSV PDB
model_8 -1.4011 View CSV PDB
model_11 -1.4071 View CSV PDB
model_10 -1.4167 View CSV PDB
model_5 -1.4211 View CSV PDB
model_9 -1.4271 View CSV PDB
model_4 -1.445 View CSV PDB