Project name: y-syn

Status: done

Started: 2025-05-14 20:26:06
Chain sequence(s) A: MDVFKKGFSIAKEGVVGAVEKTKQGVTEAAEKTKEGVMYVGAKTKENVVQSVTSVAEKTKEQANAVSEAVVSSVNTVATKTVEEAENIAVTSGVVRKEDLRPSAPQQEGEASKEKEEVAEEAQSGGD
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.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:15:44)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:15:44)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:45)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:45)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:45)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:46)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:46)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:47)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:47)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:47)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:48)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:48)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:49)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:53)
Show buried residues
Minimal score value
-3.9826
Maximal score value
2.437
Average score
-0.7309
Total score value
-92.828
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 0.1740
2 D A -1.0669
3 V A 0.5556
4 F A 1.2689
5 K A -0.5888
6 K A -0.9238
7 G A 0.0216
8 F A 1.1510
9 S A -0.2263
10 I A 0.6613
11 A A 0.1897
12 K A -0.8461
13 E A -0.9010
14 G A 0.1773
15 V A 1.2689
16 V A 0.5713
17 G A -0.7145
18 A A -0.2414
19 V A 0.1424
20 E A -2.1584
21 K A -2.4974
22 T A -1.7180
23 K A -2.7330
24 Q A -2.8828
25 G A -1.5619
26 V A -0.4880
27 T A -1.6479
28 E A -3.0590
29 A A -2.0066
30 A A -2.4929
31 E A -3.8423
32 K A -3.9826
33 T A -2.3178
34 K A -2.9011
35 E A -2.3306
36 G A -0.3481
37 V A 1.4320
38 M A 1.3442
39 Y A 1.1708
40 V A 1.0509
41 G A 0.2497
42 A A -0.6313
43 K A -2.0740
44 T A -1.1164
45 K A -2.1498
46 E A -2.4102
47 N A -1.3410
48 V A 0.6460
49 V A 1.2704
50 Q A 0.1944
51 S A 0.9588
52 V A 2.4141
53 T A 0.9144
54 S A 0.4572
55 V A 0.6591
56 A A -0.7324
57 E A -2.3991
58 K A -3.2249
59 T A -2.7111
60 K A -3.5694
61 E A -3.5806
62 Q A -3.1161
63 A A -2.0824
64 N A -2.6194
65 A A -0.9444
66 V A 0.8386
67 S A 0.1668
68 E A -0.5584
69 A A 0.9548
70 V A 2.4370
71 V A 2.3532
72 S A 1.1145
73 S A 1.6823
74 V A 2.2613
75 N A 0.5100
76 T A 0.5905
77 V A 1.4235
78 A A -0.1714
79 T A 0.0000
80 K A -1.6623
81 T A -1.3691
82 V A 0.0000
83 E A -2.0549
84 E A -2.1401
85 A A -0.9270
86 E A 0.0000
87 N A -0.6237
88 I A 1.1621
89 A A 0.8475
90 V A 1.2227
91 T A 0.8663
92 S A 0.6697
93 G A 0.6608
94 V A 1.1497
95 V A 0.8915
96 R A -1.2182
97 K A -2.3189
98 E A -1.7611
99 D A -1.5388
100 L A -0.2148
101 R A 0.0000
102 P A -0.4103
103 S A -0.6278
104 A A 0.0000
105 P A -1.3000
106 Q A -1.6716
107 Q A -1.5062
108 E A 0.0000
109 G A -1.1200
110 E A -2.3923
111 A A -1.9707
112 S A -1.8047
113 K A 0.0000
114 E A -2.7461
115 K A -3.5318
116 E A 0.0000
117 E A -2.6203
118 V A -0.5871
119 A A -1.5445
120 E A -1.8645
121 E A -1.9804
122 A A -1.8362
123 Q A 0.0000
124 S A -2.0506
125 G A -1.8087
126 G A -1.8514
127 D A -2.6112
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, -0.7309 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_10 -0.7309 View CSV PDB
model_5 -0.7411 View CSV PDB
model_4 -0.7675 View CSV PDB
model_9 -0.802 View CSV PDB
model_0 -0.8026 View CSV PDB
model_1 -0.8078 View CSV PDB
model_8 -0.8178 View CSV PDB
model_2 -0.8187 View CSV PDB
CABS_average -0.8525 View CSV PDB
model_3 -0.8593 View CSV PDB
model_7 -0.9212 View CSV PDB
model_6 -0.9919 View CSV PDB
input -1.1107 View CSV PDB
model_11 -1.1691 View CSV PDB