Project name: LVS

Status: done

Started: 2025-12-11 12:14:46
Chain sequence(s) H: EVQLLESGGGLVQPGGSLRLSCAASGYTNRLKCMGWFRQAPGKERELVSISTGTGNTYYADSVKGRFTISRDNSKNTLYLQMNSLKAEDTAVYYCAADVRPDGTTCHYNSRGQGTLVTVSS
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                                                (00:00:38)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:14:59)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:14:59)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:15:00)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:15:00)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:15:01)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:15:01)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:15:01)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:15:02)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:15:02)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:15:02)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:15:03)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:15:03)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:15:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:15:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:15:06)
Show buried residues
Minimal score value
-4.0541
Maximal score value
1.739
Average score
-0.7099
Total score value
-85.9028
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 -1.3615
2 V H 0.0000
3 Q H -1.5899
4 L H 0.0000
5 L H 0.4682
6 E H -0.2777
7 S H -0.6379
8 G H -0.7662
9 G H -0.1889
11 G H 0.0000
12 L H 0.5259
13 V H 0.0000
14 Q H -0.3204
15 P H -0.3095
16 G H -0.6222
17 G H -0.7806
18 S H -1.1999
19 L H 0.0000
20 R H -2.1611
21 L H 0.0000
22 S H -0.5972
23 C H 0.0000
24 A H -0.1648
25 A H 0.0000
26 S H -0.7868
27 G H -1.1664
28 Y H 0.0000
29 T H -1.1990
30 N H -1.0723
35 R H -0.2591
36 L H 0.5874
37 K H 0.0000
38 C H 0.0000
39 M H 0.0000
40 G H 0.0000
41 W H 0.0000
42 F H 0.0000
43 R H 0.0000
44 Q H -1.9128
45 A H -2.0265
46 P H -1.8722
47 G H -2.0774
48 K H -3.5778
49 E H -4.0541
50 R H -3.7277
51 E H -2.5671
53 L H -0.6291
54 V H 0.0000
55 S H 0.0000
56 I H 0.0000
57 S H 0.0000
58 T H -0.3486
59 G H -0.1963
62 T H -0.3239
63 G H -0.3833
64 N H -0.0754
65 T H 0.5663
66 Y H 1.6538
67 Y H 1.7390
68 A H 0.5114
69 D H -0.6475
70 S H -0.7478
71 V H 0.0000
72 K H -1.7114
74 G H -1.5435
75 R H -2.2678
76 F H -0.7255
77 T H -0.0836
78 I H 0.3609
79 S H -0.9408
80 R H -2.6802
81 D H -2.9639
82 N H -2.4641
83 S H -1.9743
84 K H -2.7024
85 N H -2.1282
86 T H -1.5056
87 L H 0.0000
88 Y H -0.9490
89 L H 0.0000
90 Q H -1.4088
91 M H 0.0000
92 N H -1.8906
93 S H 0.0000
94 L H 0.2711
95 K H -0.8240
96 A H -1.0723
97 E H -2.1044
98 D H -1.5098
99 T H -0.4560
100 A H 0.0000
101 V H 0.5040
102 Y H 0.0000
103 Y H -0.4541
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 D H 0.0000
108 V H -0.4957
109 R H -1.2604
110 P H -1.0461
111 D H -1.7725
111A G H -0.9542
112A T H -0.7720
112 T H -0.5491
113 C H 0.0000
114 H H -1.4149
115 Y H -1.5066
116 N H -2.0712
117 S H -2.1194
118 R H -2.6013
119 G H 0.0000
120 Q H -1.4023
121 G H -0.4770
122 T H 0.0000
123 L H 1.0423
124 V H 0.0000
125 T H 0.1084
126 V H 0.0000
127 S H -0.5303
128 S H -0.2793
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, -0.7099 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_6 -0.7099 View CSV PDB
model_5 -0.7696 View CSV PDB
model_2 -0.7717 View CSV PDB
model_0 -0.7817 View CSV PDB
model_4 -0.7868 View CSV PDB
model_7 -0.7897 View CSV PDB
model_1 -0.8418 View CSV PDB
CABS_average -0.8444 View CSV PDB
model_3 -0.8523 View CSV PDB
input -0.859 View CSV PDB
model_8 -0.8954 View CSV PDB
model_11 -0.9645 View CSV PDB
model_10 -0.9723 View CSV PDB
model_9 -0.9976 View CSV PDB