Project name: a-syn

Status: done

Started: 2025-05-13 19:19:46
Chain sequence(s) A: MDVFMKGLSKAKEGVVAAAEKTKQGVAEAAGKTKEGVLYVGSKTKEGVVHGVATVAEKTKEQVTNVGGAVVTGVTAVAQKTVEGAGSIAAATGFVKKDQLGKNEEGAPQEGILEDMPVDPDNEAYEMPSEEGYQDYEPEA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage No
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]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:20:12)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:20:13)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:20:13)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:20:13)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:20:14)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:20:14)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:20:15)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:20:15)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:20:16)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:20:16)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:20:17)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:20:17)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:20:18)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:20:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:20:22)
Show buried residues
Minimal score value
-3.3025
Maximal score value
2.4436
Average score
-0.5963
Total score value
-83.4779
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 0.6963
2 D A 0.0006
3 V A 2.0192
4 F A 2.3104
5 M A 1.1312
6 K A -0.5214
7 G A -0.2905
8 L A 0.4370
9 S A -0.7066
10 K A -1.9377
11 A A -1.0477
12 K A -1.0764
13 E A -1.8239
14 G A -0.8831
15 V A 0.6270
16 V A 0.6149
17 A A -0.2893
18 A A -0.7133
19 A A -1.4012
20 E A -2.7001
21 K A -2.9165
22 T A -2.2713
23 K A -3.2221
24 Q A -3.2098
25 G A -1.6972
26 V A -0.2555
27 A A -1.4667
28 E A -2.7423
29 A A -1.6782
30 A A -1.6933
31 G A -2.2990
32 K A -3.0898
33 T A -1.8982
34 K A -2.1058
35 E A -1.6715
36 G A 0.0737
37 V A 1.6509
38 L A 1.8226
39 Y A 1.8208
40 V A 1.9987
41 G A 0.4362
42 S A -0.1556
43 K A -0.6137
44 T A -0.8186
45 K A -1.9625
46 E A -1.9304
47 G A -0.9289
48 V A 0.7487
49 V A 0.6648
50 H A -0.0289
51 G A 0.7404
52 V A 2.2160
53 A A 0.7444
54 T A 0.0869
55 V A 0.5869
56 A A -0.9545
57 E A -2.7224
58 K A -3.1720
59 T A -2.2812
60 K A -2.9816
61 E A -2.9775
62 Q A -2.0566
63 V A -0.1503
64 T A -0.7375
65 N A -1.0639
66 V A 1.3739
67 G A 1.1280
68 G A 0.8500
69 A A 1.2723
70 V A 2.0196
71 V A 2.4436
72 T A 1.2506
73 G A 0.4459
74 V A 0.0000
75 T A -0.3036
76 A A -0.3798
77 V A -0.5118
78 A A 0.0000
79 Q A -2.2666
80 K A -2.4744
81 T A -1.3633
82 V A -0.8615
83 E A -2.4291
84 G A -1.3715
85 A A 0.0000
86 G A -0.1407
87 S A -0.4311
88 I A 0.3643
89 A A 0.3848
90 A A 0.0839
91 A A 0.3884
92 T A 0.5225
93 G A 0.7764
94 F A 1.5039
95 V A 0.7803
96 K A -1.7641
97 K A -2.2325
98 D A -3.1042
99 Q A -2.8144
100 L A -1.7779
101 G A -2.4280
102 K A -3.3025
103 N A 0.0000
104 E A -1.4218
105 E A 0.0000
106 G A 0.0000
107 A A 0.0585
108 P A -0.8633
109 Q A -1.1249
110 E A -1.8642
111 G A -0.2782
112 I A 0.3910
113 L A 0.9090
114 E A -0.5584
115 D A -1.3462
116 M A -0.5375
117 P A -0.0195
118 V A 1.3759
119 D A -0.1767
120 P A 0.0000
121 D A 0.0000
122 N A -0.8704
123 E A -1.8992
124 A A -0.4266
125 Y A 0.4754
126 E A -0.0145
127 M A -0.2209
128 P A -0.9897
129 S A 0.0000
130 E A -2.5414
131 E A -1.8968
132 G A -1.0502
133 Y A 0.2544
134 Q A 0.0000
135 D A -2.1363
136 Y A 0.0000
137 E A -1.8398
138 P A -0.8569
139 E A -0.3045
140 A A 0.3813
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, -0.5963 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_3 -0.5963 View CSV PDB
input -0.6974 View CSV PDB
model_0 -0.7817 View CSV PDB
model_5 -0.7825 View CSV PDB
model_8 -0.7846 View CSV PDB
model_7 -0.7961 View CSV PDB
model_1 -0.8418 View CSV PDB
model_10 -0.8525 View CSV PDB
CABS_average -0.8536 View CSV PDB
model_2 -0.859 View CSV PDB
model_9 -0.9348 View CSV PDB
model_4 -0.9426 View CSV PDB
model_6 -0.9793 View CSV PDB
model_11 -1.0922 View CSV PDB