Project name: Designed Nanobody

Status: done

Started: 2026-07-10 21:41:54
Chain sequence(s) B: QVQLVESGGGLVQPGGSLRLSCAASGFPFSSYGMGWVRQAPGKGLEWVSGINWSGGSTGYADSVKGRFTISRDNAKNTLYLQMNSLRAEDTAVYYCADGLLFSYDDWGQGTQVTVSS
input PDB
Selected Chain(s) B
Distance of aggregation 10 Å
FoldX usage No
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 B chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:12:26)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:12:28)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:28)
Show buried residues
Minimal score value
-2.4268
Maximal score value
2.9342
Average score
-0.2597
Total score value
-30.3875
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 Q B -1.1737
2 V B 0.0000
3 Q B -1.4083
4 L B 0.0000
5 V B 0.1544
6 E B -0.3867
7 S B -0.9813
8 G B -1.1125
9 G B -0.4053
10 G B 0.2602
11 L B 2.1234
12 V B 2.4691
13 Q B 0.0000
14 P B -0.7484
15 G B -0.9426
16 G B -0.5589
17 S B -0.9451
18 L B 0.0000
19 R B -2.3069
20 L B 0.0000
21 S B -0.6135
22 C B 0.0000
23 A B -0.4949
24 A B 0.0000
25 S B -0.9242
26 G B -1.2688
27 F B 0.0000
28 P B -0.9844
29 F B 0.0000
30 S B -0.5624
31 S B 0.2381
32 Y B 0.0000
33 G B 0.2768
34 M B 0.0000
35 G B -0.0844
36 W B 0.0000
37 V B 0.8341
38 R B 0.0000
39 Q B -0.0676
40 A B 0.0000
41 P B -0.5167
42 G B -1.0535
43 K B -1.0551
44 G B -0.0870
45 L B 1.1228
46 E B 0.5802
47 W B 1.4227
48 V B 0.0000
49 S B 0.0000
50 G B 0.1939
51 I B 0.0000
52 N B -0.7421
53 W B 0.1453
54 S B -0.2583
55 G B -0.5455
56 G B -0.7107
57 S B -0.6265
58 T B -0.2145
59 G B 0.0960
60 Y B 1.2159
61 A B 0.8052
62 D B 0.5148
63 S B 0.5569
64 V B 1.3190
65 K B 0.0000
66 G B -0.6588
67 R B 0.0000
68 F B 0.0000
69 T B -0.3420
70 I B -0.0219
71 S B -0.8759
72 R B -1.9700
73 D B -2.3242
74 N B -2.0546
75 A B -1.5772
76 K B -2.4268
77 N B -2.3151
78 T B 0.0000
79 L B 0.0000
80 Y B -0.6216
81 L B 0.0000
82 Q B -1.4652
83 M B 0.0000
84 N B -1.9290
85 S B -1.3575
86 L B 0.0000
87 R B -1.2930
88 A B 0.0000
89 E B -1.2340
90 D B -1.9656
91 T B -1.0542
92 A B 0.0000
93 V B -0.0060
94 Y B 0.0000
95 Y B -0.1984
96 C B 0.0000
97 A B -0.6076
98 D B 0.0000
99 G B 0.7897
100 L B 1.7328
101 L B 2.8806
102 F B 2.9342
103 S B 0.0000
104 Y B 1.4167
105 D B -0.7579
106 D B -1.8570
107 W B -1.0803
108 G B -1.2006
109 Q B -1.1045
110 G B -0.9294
111 T B 0.0000
112 Q B -0.9033
113 V B 0.0000
114 T B 0.0000
115 V B 1.2062
116 S B 0.1765
117 S B 0.0584
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, -0.2597 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_8 -0.2597 View CSV PDB
model_2 -0.2699 View CSV PDB
model_1 -0.2828 View CSV PDB
model_5 -0.3201 View CSV PDB
model_7 -0.3237 View CSV PDB
model_4 -0.3435 View CSV PDB
model_11 -0.3478 View CSV PDB
CABS_average -0.3487 View CSV PDB
model_6 -0.37 View CSV PDB
model_3 -0.3746 View CSV PDB
model_9 -0.413 View CSV PDB
model_10 -0.4169 View CSV PDB
model_0 -0.4626 View CSV PDB
input -0.5085 View CSV PDB