Project name: L41A

Status: done

Started: 2026-03-07 01:36:34
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:05:11)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:36:50)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:36:51)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:36:52)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:36:53)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:36:54)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:36:54)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:36:55)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:36:56)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:36:57)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:36:58)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:36:59)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:36:59)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:37:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:37:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:05)
Show buried residues
Minimal score value
-3.1472
Maximal score value
0.0
Average score
-1.2127
Total score value
-224.3455
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 -0.5974
2 D A -1.9543
3 V A -1.3169
4 D A -2.7255
5 E A -2.7418
6 M A 0.0000
7 L A 0.0000
8 K A -2.5822
9 Q A -1.9717
10 V A 0.0000
11 E A -2.2111
12 I A -1.4174
13 L A 0.0000
14 R A -2.1913
15 R A -2.0466
16 L A -0.7313
17 G A -1.2534
18 A A 0.0000
19 K A -1.8880
20 Q A -1.1619
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -1.1786
25 S A -1.3539
26 D A -2.5804
27 D A -1.6939
28 W A -1.3595
29 R A -2.1487
30 I A -1.5353
31 L A 0.0000
32 Q A -1.6428
33 E A -2.3433
34 A A 0.0000
35 L A -1.8165
36 K A -2.5967
37 K A -2.6675
38 G A -1.9764
39 G A -1.4253
40 D A -1.2671
41 I A 0.0000
42 A A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A -1.5412
46 A A -2.1127
47 T A -1.6021
48 D A -2.4201
49 V A -1.2590
50 D A -2.6238
51 E A -2.8644
52 M A 0.0000
53 L A -2.3544
54 K A -2.6419
55 Q A 0.0000
56 V A 0.0000
57 E A -3.1472
58 I A -1.8255
59 L A 0.0000
60 R A -2.5511
61 R A -2.3660
62 L A -0.9306
63 G A -1.5744
64 A A 0.0000
65 K A -1.9409
66 Q A -1.1917
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -1.1142
71 S A -1.3841
72 D A -2.4556
73 D A -1.7995
74 W A -1.5039
75 R A -2.0671
76 I A -1.3576
77 L A 0.0000
78 Q A -1.5340
79 E A -2.0770
80 A A 0.0000
81 L A -1.8696
82 K A -2.6808
83 K A -2.9016
84 G A -2.0632
85 G A -1.5377
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 -1.3990
92 A A -1.6813
93 T A -1.4209
94 D A -2.3678
95 V A -1.8270
96 D A -2.8577
97 E A -3.0808
98 M A 0.0000
99 L A -2.1311
100 K A -2.3778
101 Q A 0.0000
102 V A 0.0000
103 E A -1.5844
104 I A -0.9701
105 L A 0.0000
106 R A -1.7029
107 R A -1.7023
108 L A -0.4759
109 G A -1.1809
110 A A 0.0000
111 K A -1.8966
112 Q A -1.2182
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A 0.0000
117 S A -1.2548
118 D A -2.4929
119 D A -1.8072
120 W A -1.3865
121 R A -2.1184
122 I A -1.3185
123 L A 0.0000
124 Q A -1.5976
125 E A -2.2777
126 A A 0.0000
127 L A 0.0000
128 K A -2.6231
129 K A -2.3351
130 G A -1.8017
131 G A 0.0000
132 D A -1.3785
133 I A 0.0000
134 A A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.8597
138 A A -2.1399
139 T A -1.7126
140 D A -2.4392
141 V A -1.6419
142 D A -2.8108
143 E A -3.1216
144 M A 0.0000
145 L A -2.0843
146 K A -2.2855
147 Q A 0.0000
148 V A 0.0000
149 E A -2.1913
150 I A -1.1976
151 L A 0.0000
152 R A -2.2381
153 R A -1.9586
154 L A -0.4646
155 G A -1.1708
156 A A -1.5960
157 K A -1.9703
158 Q A -1.2473
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -0.7744
163 S A -0.8986
164 D A -1.0125
165 D A -1.3100
166 W A -1.0311
167 R A -1.6504
168 I A -1.1425
169 L A 0.0000
170 Q A -1.3363
171 E A -1.7022
172 A A 0.0000
173 L A -1.5234
174 K A -2.4670
175 K A -2.4812
176 G A -1.9715
177 G A -1.3705
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 -0.6793
184 A A -0.6950
185 T A -0.2332
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, -1.2127 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 -1.2127 View CSV PDB
model_9 -1.288 View CSV PDB
model_3 -1.2906 View CSV PDB
model_4 -1.3249 View CSV PDB
model_5 -1.3563 View CSV PDB
model_11 -1.3777 View CSV PDB
model_6 -1.388 View CSV PDB
CABS_average -1.3926 View CSV PDB
model_1 -1.3975 View CSV PDB
model_0 -1.398 View CSV PDB
model_2 -1.4361 View CSV PDB
model_10 -1.4529 View CSV PDB
model_8 -1.4802 View CSV PDB
model_7 -1.5206 View CSV PDB