Project name: LAAS

Status: done

Started: 2025-12-11 12:14:09
Chain sequence(s) H: EVQLLESGGGLVQPGGSLRLSCAASGYTNRLKCMGWFRQAPGKERELAASISTGTGNTYYADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAADVRPDGTTCHYNSRGQGTLVTVSS
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                                          (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:57)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:15:33)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:15:34)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:34)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:35)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:35)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:35)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:36)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:36)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:36)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:36)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:37)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:37)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:38)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:39)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:40)
Show buried residues
Minimal score value
-3.5996
Maximal score value
2.0037
Average score
-0.4225
Total score value
-51.5443
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 -1.7517
2 V H -1.0286
3 Q H -1.3365
4 L H -0.7006
5 L H 0.4958
6 E H -0.4984
7 S H -0.2695
8 G H -0.0913
9 G H 0.4311
11 G H 0.5220
12 L H 1.4193
13 V H 0.0000
14 Q H -0.7995
15 P H -0.9845
16 G H -0.9021
17 G H -0.6573
18 S H -0.6105
19 L H 0.0000
20 R H -0.8862
21 L H 0.0000
22 S H -0.2221
23 C H 0.0000
24 A H 0.0088
25 A H 0.0000
26 S H -0.5812
27 G H -0.7743
28 Y H -0.3988
29 T H -0.8943
30 N H -1.7648
35 R H 0.0000
36 L H 0.0000
37 K H -0.7743
38 C H 0.0000
39 M H 0.0000
40 G H 0.0000
41 W H 0.0000
42 F H -0.6002
43 R H 0.0000
44 Q H -2.2457
45 A H -1.9686
46 P H -1.8384
47 G H -1.8380
48 K H -2.6427
49 E H -3.5996
50 R H -3.4945
51 E H -2.0145
52 L H -0.2063
53 A H 0.0000
54 A H 0.0000
55 S H 0.0000
56 I H 0.0000
57 S H 0.0000
58 T H 0.0000
59 G H -1.5032
62 T H -1.2174
63 G H -1.2113
64 N H -0.7937
65 T H 0.4786
66 Y H 1.9461
67 Y H 2.0037
68 A H 1.1955
69 D H 0.3761
70 S H 0.2827
71 V H 1.3820
72 K H 0.4173
74 G H 0.0987
75 R H 0.0000
76 F H 0.9380
77 T H 0.7833
78 I H 0.6027
79 S H -0.1739
80 R H -1.2071
81 D H -1.9758
82 N H -2.1310
83 S H -1.7690
84 K H -2.4333
85 N H 0.0000
86 T H -0.9271
87 L H 0.0000
88 Y H -0.1500
89 L H 0.0000
90 Q H -0.4626
91 M H 0.0000
92 N H -0.8521
93 S H 0.0000
94 L H 0.1421
95 K H -1.4599
96 A H 0.0000
97 E H -0.6638
98 D H 0.0000
99 T H 0.2515
100 A H 0.3134
101 V H 0.5444
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 D H 0.0000
108 V H 0.7149
109 R H -0.3997
110 P H -0.9479
111 D H -1.8050
111A G H -1.5835
112A T H -0.8398
112 T H -0.4435
113 C H 0.2345
114 H H -0.0458
115 Y H 0.3121
116 N H -1.1318
117 S H -1.5803
118 R H -2.2259
119 G H -1.6295
120 Q H -1.4379
121 G H -0.2182
122 T H 0.0000
123 L H 1.4563
124 V H 0.0000
125 T H 1.1063
126 V H 0.5911
127 S H -0.2247
128 S H -0.7729
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, -0.4225 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 -0.4225 View CSV PDB
model_11 -0.4988 View CSV PDB
model_5 -0.5113 View CSV PDB
model_1 -0.5318 View CSV PDB
model_7 -0.535 View CSV PDB
CABS_average -0.5879 View CSV PDB
model_6 -0.5995 View CSV PDB
model_4 -0.6019 View CSV PDB
model_8 -0.6047 View CSV PDB
model_9 -0.6299 View CSV PDB
model_10 -0.6584 View CSV PDB
model_3 -0.706 View CSV PDB
model_0 -0.7544 View CSV PDB
input -0.802 View CSV PDB