Project name: LVAS

Status: done

Started: 2025-12-11 12:14:28
Chain sequence(s) H: EVQLLESGGGLVQPGGSLRLSCAASGYTNRLKCMGWFRQAPGKERELVASISTGTGNTYYADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAADVRPDGTTCHYNSRGQGTLVTVSS
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]                                                (00:00:00)
[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 H 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                                                (00:00:54)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:15:09)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:15:10)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:10)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:10)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:11)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:11)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:12)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:12)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:12)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:13)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:13)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:13)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:14)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:16)
Show buried residues
Minimal score value
-3.3109
Maximal score value
1.9734
Average score
-0.7103
Total score value
-86.6585
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 E H -2.3126
2 V H 0.0000
3 Q H -1.6611
4 L H 0.0000
5 L H 0.1596
6 E H 0.0000
7 S H -0.3075
8 G H -0.1703
9 G H 0.0902
11 G H 0.4863
12 L H 1.3370
13 V H 0.0000
14 Q H -0.8704
15 P H -1.2248
16 G H -0.9059
17 G H -0.4987
18 S H -0.8873
19 L H -0.9763
20 R H -1.9625
21 L H 0.0000
22 S H -0.2452
23 C H 0.0000
24 A H -0.0083
25 A H 0.0000
26 S H -0.8071
27 G H -0.6799
28 Y H -0.2120
29 T H -0.7407
30 N H -1.7526
35 R H -1.3455
36 L H -0.6830
37 K H -1.4780
38 C H 0.0000
39 M H 0.0000
40 G H 0.3771
41 W H 0.0000
42 F H -0.1063
43 R H 0.0000
44 Q H -1.5603
45 A H 0.0000
46 P H -1.9721
47 G H -1.8781
48 K H -2.6712
49 E H -3.3109
50 R H -2.9348
51 E H -1.3180
52 L H 0.8104
53 V H 0.0000
54 A H 0.0000
55 S H 0.0000
56 I H 0.3156
57 S H 0.0000
58 T H -0.7024
59 G H -1.2163
62 T H -1.3905
63 G H -1.0830
64 N H -0.3599
65 T H 0.6681
66 Y H 1.9734
67 Y H 1.8591
68 A H 1.0195
69 D H -0.1590
70 S H -0.4798
71 V H -1.2501
72 K H -2.5161
74 G H -2.3117
75 R H -2.5497
76 F H 0.0000
77 T H -0.4778
78 I H 0.3674
79 S H 0.0075
80 R H -1.0108
81 D H -1.7808
82 N H -2.5783
83 S H -2.0484
84 K H -2.6798
85 N H -1.7782
86 T H -0.8830
87 L H 0.0000
88 Y H 0.3072
89 L H 0.0000
90 Q H -1.3159
91 M H 0.0000
92 N H -2.4045
93 S H -1.7460
94 L H 0.0000
95 K H -1.6464
96 A H -1.2230
97 E H -1.6141
98 D H -2.2241
99 T H -0.7953
100 A H 0.0000
101 V H 0.0039
102 Y H 0.0000
103 Y H -0.4034
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 D H 0.0000
108 V H -0.9351
109 R H -2.4018
110 P H -1.9766
111 D H -2.6852
111A G H -1.8607
112A T H -1.4142
112 T H -0.3510
113 C H -0.0350
114 H H -0.5652
115 Y H -0.2221
116 N H -1.5980
117 S H -1.9753
118 R H -2.5158
119 G H 0.0000
120 Q H -1.3725
121 G H -0.6064
122 T H 0.0000
123 L H 1.3958
124 V H 0.0000
125 T H 0.1562
126 V H 0.0000
127 S H -0.6606
128 S H -0.7076
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, -0.7103 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_7 -0.7103 View CSV PDB
model_11 -0.7334 View CSV PDB
model_6 -0.7556 View CSV PDB
model_4 -0.7565 View CSV PDB
model_2 -0.789 View CSV PDB
CABS_average -0.7969 View CSV PDB
model_3 -0.8149 View CSV PDB
model_8 -0.8184 View CSV PDB
model_10 -0.8223 View CSV PDB
model_0 -0.8238 View CSV PDB
model_5 -0.8361 View CSV PDB
input -0.842 View CSV PDB
model_1 -0.8438 View CSV PDB
model_9 -0.8593 View CSV PDB