Project name: alpha-synuclein

Status: done

Started: 2026-04-20 15:28:14
Chain sequence(s) A: MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA
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                                                (00:02:13)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:15:22)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:15:23)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:23)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:24)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:24)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:26)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:26)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:26)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:27)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:29)
Show buried residues
Minimal score value
-3.5305
Maximal score value
3.2003
Average score
-0.5061
Total score value
-70.8521
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 0.6588
2 D A -0.6714
3 V A 0.1190
4 F A 0.5731
5 M A 0.8042
6 K A -0.9727
7 G A -0.3626
8 L A 0.6450
9 S A -0.6915
10 K A -1.2084
11 A A -0.2128
12 K A -1.5642
13 E A -1.4929
14 G A 0.6022
15 V A 1.0744
16 V A 0.9097
17 A A 0.1760
18 A A -0.0375
19 A A -0.6395
20 E A -1.7618
21 K A -1.0522
22 T A -0.9896
23 K A -2.1615
24 Q A -1.4991
25 G A -0.6266
26 V A 0.4370
27 A A -0.1879
28 E A -0.5536
29 A A -0.5344
30 A A -0.7759
31 G A -0.9668
32 K A -1.5860
33 T A -1.0262
34 K A -1.2300
35 E A -0.2238
36 G A 0.6078
37 V A 1.7927
38 L A 1.1342
39 Y A 1.6522
40 V A 2.2688
41 G A 0.7216
42 S A -0.8053
43 K A -1.9669
44 T A -2.1475
45 K A -2.6342
46 E A -2.9347
47 G A -1.7049
48 V A 0.0000
49 V A -0.1060
50 H A -0.6266
51 G A -0.2356
52 V A 0.8307
53 A A 0.2451
54 T A -0.4881
55 V A -0.8739
56 A A -1.6069
57 E A -2.6756
58 K A -2.3569
59 T A -2.1385
60 K A -2.8905
61 E A -2.8773
62 Q A -1.6263
63 V A -0.1697
64 T A -0.8339
65 N A -1.0970
66 V A 0.5900
67 G A 0.7324
68 G A 0.2867
69 A A 1.6325
70 V A 2.9830
71 V A 3.2003
72 T A 1.9446
73 G A 1.8916
74 V A 3.0491
75 T A 1.5699
76 A A 0.9152
77 V A 1.9534
78 A A 0.7805
79 Q A -0.1333
80 K A -0.4080
81 T A -0.0873
82 V A 0.7989
83 E A 0.0934
84 G A -0.0357
85 A A 0.5057
86 G A 0.4786
87 S A 1.1058
88 I A 1.9705
89 A A 1.0284
90 A A 1.1811
91 A A 1.4255
92 T A 0.8226
93 G A 0.9403
94 F A 1.8351
95 V A 1.7628
96 K A -0.0019
97 K A 0.0000
98 D A -2.3669
99 Q A 0.0000
100 L A -0.6527
101 G A -1.4013
102 K A -2.8710
103 N A -3.3417
104 E A -3.2936
105 E A -3.4929
106 G A -2.1992
107 A A -1.1756
108 P A -1.1256
109 Q A -1.6301
110 E A -1.7731
111 G A -0.3734
112 I A 1.6150
113 L A 1.5051
114 E A 0.0000
115 D A -0.7364
116 M A -0.4518
117 P A -0.6247
118 V A -1.2785
119 D A -2.2812
120 P A -2.1616
121 D A -3.0959
122 N A -3.5305
123 E A -3.1029
124 A A -3.0221
125 Y A 0.0000
126 E A -2.2235
127 M A 0.0000
128 P A -1.2820
129 S A -1.6074
130 E A -2.1516
131 E A 0.0000
132 G A -0.2708
133 Y A 0.1231
134 Q A 0.0000
135 D A -2.0462
136 Y A -2.2622
137 E A -2.9078
138 P A -2.7779
139 E A -3.0810
140 A A -1.7412
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, -0.5061 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
model_7 -0.5061 View CSV PDB
model_6 -0.5073 View CSV PDB
model_8 -0.535 View CSV PDB
model_4 -0.5686 View CSV PDB
model_10 -0.6196 View CSV PDB
model_11 -0.6217 View CSV PDB
model_5 -0.6392 View CSV PDB
model_9 -0.6581 View CSV PDB
CABS_average -0.6588 View CSV PDB
model_1 -0.7071 View CSV PDB
model_3 -0.7418 View CSV PDB
model_2 -0.8491 View CSV PDB
input -0.8548 View CSV PDB
model_0 -0.9522 View CSV PDB