Project name: S04

Status: done

Started: 2025-12-11 12:15:06
Chain sequence(s) H: DVQLQESGGGLVQPGGSLRLSCAASGFPFNIAAMSWVRQAPGKGLEWVSTINKDGDTYYVDSVKGRFTISRDNAKDTLYLELNGLKPEDTAMYYCALLRGTRGPSNANSPDVNYRGQGTQVTVSS
input PDB
Selected Chain(s) H
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 H 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                                                (00:00:54)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:15:21)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:15:21)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:22)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:22)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:22)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:23)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:23)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:24)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:24)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:24)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:25)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:28)
Show buried residues
Minimal score value
-3.3158
Maximal score value
0.9931
Average score
-0.8689
Total score value
-108.6169
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 D H -2.5639
2 V H 0.0000
3 Q H -2.3941
4 L H 0.0000
5 Q H -2.2881
6 E H 0.0000
7 S H -1.3416
8 G H -1.1125
9 G H -0.9049
11 G H 0.0000
12 L H 0.6088
13 V H 0.0000
14 Q H -1.2545
15 P H -1.0662
16 G H -1.1669
17 G H -0.8258
18 S H -0.9703
19 L H 0.0000
20 R H -1.5314
21 L H 0.0000
22 S H -0.7469
23 C H 0.0000
24 A H -1.1444
25 A H -1.6361
26 S H -1.5100
27 G H -0.9766
28 F H -0.8389
29 P H -1.3464
30 F H 0.0000
35 N H -2.4905
36 I H 0.0000
37 A H -2.2067
38 A H 0.0000
39 M H 0.0000
40 S H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -1.1863
45 A H 0.0000
46 P H -1.4902
47 G H -1.4550
48 K H -2.0953
49 G H -0.9238
50 L H 0.4413
51 E H -0.5655
52 W H -0.0173
53 V H 0.0000
54 S H 0.0000
55 T H 0.0000
56 I H 0.0000
57 N H 0.0000
58 K H -3.2371
59 D H -3.3158
63 G H -2.1161
64 D H -1.5050
65 T H -0.1745
66 Y H 0.6218
67 Y H 0.7583
68 V H 0.9931
69 D H -0.8837
70 S H -0.5123
71 V H 0.0000
72 K H -1.2451
74 G H -1.3212
75 R H -1.4289
76 F H 0.0451
77 T H -0.1266
78 I H 0.1941
79 S H -0.3869
80 R H -1.8268
81 D H -2.8262
82 N H -3.0737
83 A H -2.1506
84 K H -2.7769
85 D H -2.3545
86 T H -1.6321
87 L H 0.0000
88 Y H -0.4491
89 L H 0.0000
90 E H -0.7130
91 L H 0.0000
92 N H 0.0000
93 G H -1.4958
94 L H 0.0000
95 K H -2.2135
96 P H 0.0000
97 E H -2.5805
98 D H -2.6556
99 T H -1.4919
100 A H 0.0000
101 M H -0.7297
102 Y H 0.0000
103 Y H -0.7399
104 C H 0.0000
105 A H 0.0000
106 L H 0.0000
107 L H 0.0000
108 R H -2.4057
109 G H -2.0378
110 T H -1.4720
111 R H -2.8324
111A G H -2.2993
111B P H -1.8642
111C S H -1.5617
112C N H 0.0000
112B A H 0.0525
112A N H 0.0196
112 S H 0.2220
113 P H 0.3901
114 D H 0.0000
115 V H 0.8642
116 N H -0.7337
117 Y H -1.4093
118 R H -2.2913
119 G H -2.2731
120 Q H -2.2961
121 G H -1.5071
122 T H 0.0000
123 Q H -1.4297
124 V H 0.0000
125 T H -0.7160
126 V H 0.0000
127 S H -1.1177
128 S H -1.5676
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, -0.8689 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_9 -0.8689 View CSV PDB
model_11 -0.8946 View CSV PDB
model_2 -0.9116 View CSV PDB
model_7 -0.9203 View CSV PDB
model_4 -0.9374 View CSV PDB
model_6 -0.9434 View CSV PDB
CABS_average -0.9466 View CSV PDB
input -0.9508 View CSV PDB
model_1 -0.9539 View CSV PDB
model_5 -0.9597 View CSV PDB
model_3 -0.9646 View CSV PDB
model_10 -0.9818 View CSV PDB
model_0 -1.0057 View CSV PDB
model_8 -1.0169 View CSV PDB