Project name: a-syn

Status: done

Started: 2025-03-05 09:11:12
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:47)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:13:39)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:13:39)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:13:40)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:13:40)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:13:40)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:13:41)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:13:41)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:13:42)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:13:42)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:13:42)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:13:43)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:13:43)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:13:43)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:13:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:46)
Show buried residues
Minimal score value
-3.7009
Maximal score value
2.7357
Average score
-0.7017
Total score value
-98.243
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 0.7525
2 D A 0.0450
3 V A 2.2140
4 F A 2.7357
5 M A 1.8390
6 K A -0.0236
7 G A 0.5911
8 L A 1.0970
9 S A -0.6915
10 K A -2.0340
11 A A -0.9859
12 K A -1.6366
13 E A -1.9316
14 G A -1.0106
15 V A 0.5715
16 V A 0.5383
17 A A -0.7650
18 A A -0.9077
19 A A -1.1630
20 E A -2.8367
21 K A -3.0608
22 T A -2.1915
23 K A -3.2421
24 Q A -3.2341
25 G A -1.8707
26 V A -0.5324
27 A A -1.3187
28 E A -2.6958
29 A A -1.8547
30 A A -1.5849
31 G A -2.5644
32 K A -3.2044
33 T A -1.9755
34 K A -2.3431
35 E A -1.8564
36 G A 0.0525
37 V A 2.0440
38 L A 2.1331
39 Y A 1.8807
40 V A 2.1728
41 G A 0.6571
42 S A -0.3023
43 K A -1.0418
44 T A -0.9046
45 K A -1.7359
46 E A -1.7525
47 G A -0.4803
48 V A 1.4269
49 V A 1.5833
50 H A 0.5073
51 G A 1.1844
52 V A 2.4455
53 A A 1.0024
54 T A 0.2307
55 V A 0.6067
56 A A -1.0629
57 E A -2.9383
58 K A -3.1468
59 T A -2.5424
60 K A -3.3094
61 E A -3.7009
62 Q A -2.5293
63 V A -0.5501
64 T A -0.9805
65 N A -1.0722
66 V A 1.1540
67 G A 0.8803
68 G A 0.7419
69 A A 0.9213
70 V A 1.8887
71 V A 2.3504
72 T A 0.7586
73 G A 0.0000
74 V A 0.0000
75 T A -0.0648
76 A A -0.8915
77 V A 0.0000
78 A A 0.0000
79 Q A -2.2010
80 K A -2.1611
81 T A 0.0000
82 V A -1.4937
83 E A -2.0390
84 G A -1.4499
85 A A 0.0000
86 G A -0.2928
87 S A -0.3581
88 I A 0.1075
89 A A 0.4675
90 A A 0.1607
91 A A 0.0301
92 T A 0.1051
93 G A 0.4514
94 F A 0.8006
95 V A 0.8962
96 K A 0.0000
97 K A 0.0000
98 D A -0.9623
99 Q A 0.0000
100 L A 0.6359
101 G A 0.0000
102 K A -2.2552
103 N A -2.3362
104 E A -2.8603
105 E A -2.4916
106 G A -1.9293
107 A A -1.5747
108 P A -1.4478
109 Q A -2.1268
110 E A -2.2306
111 G A -0.5200
112 I A 1.3951
113 L A 1.3029
114 E A -0.7595
115 D A -1.4205
116 M A -0.2865
117 P A -0.3370
118 V A 0.9475
119 D A -1.0300
120 P A -1.7279
121 D A -2.9150
122 N A -2.6530
123 E A -2.8761
124 A A -1.9228
125 Y A 0.0000
126 E A -1.9139
127 M A -0.4811
128 P A 0.0000
129 S A -1.2071
130 E A -2.3166
131 E A -1.9936
132 G A -0.9402
133 Y A 0.4630
134 Q A -0.2863
135 D A -1.3934
136 Y A -0.8716
137 E A -2.5537
138 P A -2.1145
139 E A -2.4013
140 A A -1.3590
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, -0.7017 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_8 -0.7017 View CSV PDB
model_9 -0.7365 View CSV PDB
input -0.7503 View CSV PDB
model_4 -0.8135 View CSV PDB
model_3 -0.8478 View CSV PDB
model_10 -0.8632 View CSV PDB
model_1 -0.8873 View CSV PDB
CABS_average -0.8939 View CSV PDB
model_6 -0.9261 View CSV PDB
model_2 -0.9264 View CSV PDB
model_7 -0.9658 View CSV PDB
model_5 -0.9679 View CSV PDB
model_0 -1.0333 View CSV PDB
model_11 -1.0577 View CSV PDB