Project name: PDE8B_chunga_dynamic

Status: done

Started: 2026-07-29 12:23:51
Chain sequence(s) A: MGCAPSIHVSQSGVIYCRDSDESSSPRQTTSVSQGPAAPLPGLFVQTDAADAIPPSRASGPPSVARVRRARTELGSGSSAGSAAPAATTSRGRRRHCCSSAEAETQTCYQREAGVFCGGAHRAHETDAGPYSGFADLCKGR
input PDB
Selected Chain(s) A
Distance of aggregation 5 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                                                (00:00:39)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:16:00)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:16:00)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:16:01)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:16:01)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:16:01)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:16:02)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:16:02)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:16:03)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:16:03)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:16:03)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:16:04)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:16:04)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:16:04)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:16:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:09)
Show buried residues
Minimal score value
-2.1215
Maximal score value
2.5731
Average score
-0.1266
Total score value
-17.8523
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 0.7417
2 G A -0.0355
3 C A 0.0000
4 A A 0.0135
5 P A -0.0818
6 S A 0.1541
7 I A 1.9610
8 H A 0.4794
9 V A 1.7069
10 S A 0.0171
11 Q A -1.1979
12 S A -0.4304
13 G A 0.0000
14 V A 0.0000
15 I A 0.5204
16 Y A 0.0000
17 C A 0.5372
18 R A 0.0000
19 D A -1.7938
20 S A -0.6097
21 D A -1.3405
22 E A -0.4352
23 S A -0.1088
24 S A -0.1471
25 S A 0.0000
26 P A -0.2549
27 R A 0.0000
28 Q A -0.2326
29 T A -0.1219
30 T A -0.0723
31 S A 0.3350
32 V A 1.6279
33 S A -0.0685
34 Q A -1.3168
35 G A -0.7065
36 P A -0.1434
37 A A 0.0472
38 A A 0.1756
39 P A -0.1056
40 L A 0.8701
41 P A -0.1908
42 G A -0.2200
43 L A 1.9218
44 F A 2.5731
45 V A 2.0721
46 Q A -0.0182
47 T A -0.2406
48 D A -0.5474
49 A A -0.0514
50 A A -0.3154
51 D A -1.7783
52 A A -0.2827
53 I A 0.0000
54 P A -0.0861
55 P A -0.2678
56 S A -0.0795
57 R A 0.0000
58 A A -0.0194
59 S A -0.2490
60 G A -0.2525
61 P A 0.0000
62 P A -0.2190
63 S A 0.2769
64 V A 1.7887
65 A A 0.0427
66 R A -1.8006
67 V A -0.1844
68 R A 0.0000
69 R A -1.8329
70 A A -0.4161
71 R A -0.6361
72 T A -0.1926
73 E A 0.0000
74 L A 1.5167
75 G A 0.1320
76 S A 0.0000
77 G A -0.2445
78 S A -0.1742
79 S A -0.2188
80 A A -0.0525
81 G A -0.3947
82 S A -0.2764
83 A A 0.0051
84 A A 0.0190
85 P A -0.2184
86 A A 0.0237
87 A A 0.3346
88 T A -0.0424
89 T A 0.0000
90 S A -0.2129
91 R A 0.0000
92 G A 0.0000
93 R A -1.0161
94 R A -0.8486
95 R A 0.0000
96 H A 0.0000
97 C A 0.0000
98 C A 0.0000
99 S A -0.1401
100 S A -0.2209
101 A A -0.3242
102 E A -1.7980
103 A A -0.3601
104 E A -0.3658
105 T A 0.0000
106 Q A 0.0000
107 T A 0.0000
108 C A 0.0000
109 Y A 0.7679
110 Q A -0.3525
111 R A -2.1215
112 E A -1.6655
113 A A -0.2921
114 G A -0.3048
115 V A 0.0000
116 F A 0.6137
117 C A 0.0000
118 G A -0.0841
119 G A -0.2019
120 A A -0.2134
121 H A -1.2022
122 R A -1.2826
123 A A -0.3395
124 H A -0.9698
125 E A -0.7318
126 T A -0.5072
127 D A -1.7998
128 A A -0.3571
129 G A -0.1553
130 P A 0.0143
131 Y A 0.6000
132 S A -0.0601
133 G A -0.1094
134 F A 1.8624
135 A A 0.2517
136 D A -0.6392
137 L A 1.3869
138 C A 0.1580
139 K A -1.3648
140 G A -1.0012
141 R A -1.6523
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, -0.1266 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_2 -0.1266 View CSV PDB
model_3 -0.1381 View CSV PDB
model_0 -0.1522 View CSV PDB
model_1 -0.1704 View CSV PDB
model_11 -0.1764 View CSV PDB
CABS_average -0.2239 View CSV PDB
model_5 -0.2386 View CSV PDB
model_6 -0.2407 View CSV PDB
model_10 -0.2481 View CSV PDB
model_9 -0.281 View CSV PDB
model_7 -0.2863 View CSV PDB
model_4 -0.2934 View CSV PDB
input -0.3286 View CSV PDB
model_8 -0.3354 View CSV PDB