Project name: ALX_0061_anti_HSA

Status: done

Started: 2026-03-17 09:21:36
Chain sequence(s) A: EVQLVESGGGLVQPGNSLRLSCAASGFTFSSFGMSWVRQAPGKGLEWVSSISGSGSDTLYADSVKGRFTISRDNAKTTLYLQMNSLRPEDTAVYYCTIGGSLSRSSQGTLVTVSS
input PDB
Selected Chain(s) A
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 A 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                                                (00:00:37)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:12:10)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:12:11)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:12:11)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:12:11)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:12:12)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:12:12)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:12:12)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:12:13)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:12:13)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:12:13)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:12:14)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:12:14)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:12:14)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:12:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:17)
Show buried residues
Minimal score value
-2.9927
Maximal score value
1.4923
Average score
-0.4967
Total score value
-57.1238
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 A -2.1475
2 V A 0.0000
3 Q A -1.1188
4 L A 0.0000
5 V A 1.2605
6 E A 0.4259
7 S A -0.3196
8 G A -0.3427
9 G A 0.1702
10 G A 0.2772
11 L A 1.1801
12 V A 0.0000
13 Q A -1.0947
14 P A -1.1620
15 G A -1.0985
16 N A -1.0218
17 S A -1.2423
18 L A 0.0000
19 R A -2.1378
20 L A 0.0000
21 S A -0.4951
22 C A 0.0000
23 A A 0.1053
24 A A 0.0000
25 S A -0.4349
26 G A -0.8573
27 F A -0.5370
28 T A -0.7917
29 F A 0.0000
30 S A -0.6209
31 S A -0.8922
32 F A 0.0000
33 G A -0.6635
34 M A 0.0000
35 S A 0.2214
36 W A 0.0000
37 V A 0.8690
38 R A 0.0000
39 Q A 0.3649
40 A A -0.5215
41 P A -0.6525
42 G A -1.1373
43 K A -1.4812
44 G A -0.2322
45 L A 1.1526
46 E A 0.4015
47 W A 1.1371
48 V A 0.0000
49 S A 0.0000
50 S A 0.2392
51 I A 0.0000
52 S A 0.0000
53 G A -1.4399
54 S A -1.2411
55 G A -1.2347
56 S A -1.2676
57 D A -1.7202
58 T A -0.4568
59 L A 0.7935
60 Y A 1.1312
61 A A 0.1422
62 D A -1.3501
63 S A 0.0000
64 V A 0.0000
65 K A -1.8107
66 G A -1.6956
67 R A -2.0248
68 F A 0.0000
69 T A -0.6837
70 I A 0.0000
71 S A -0.6317
72 R A -1.3556
73 D A -1.8280
74 N A -1.8381
75 A A -1.4102
76 K A -2.1594
77 T A -1.3665
78 T A -0.7407
79 L A 0.0000
80 Y A -0.5724
81 L A 0.0000
82 Q A -1.4917
83 M A 0.0000
84 N A -1.6831
85 S A -1.2345
86 L A -1.1742
87 R A -1.7336
88 P A 0.0000
89 E A -2.9927
90 D A -2.9905
91 T A 0.0000
92 A A -0.1978
93 V A 0.8188
94 Y A 0.0000
95 Y A 0.6422
96 C A 0.0000
97 T A -0.2005
98 I A 0.0000
99 G A -0.3602
100 G A -0.1717
101 S A -0.2766
102 L A 0.1572
103 S A -1.2162
104 R A -2.1761
105 S A -1.3659
106 S A -0.6591
107 Q A -0.1858
108 G A 0.2816
109 T A 0.0000
110 L A 1.4923
111 V A 0.0000
112 T A 0.0313
113 V A -0.5608
114 S A -0.8311
115 S A -1.0861
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, -0.4967 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_1 -0.4967 View CSV PDB
model_10 -0.5689 View CSV PDB
model_5 -0.6003 View CSV PDB
model_7 -0.6014 View CSV PDB
model_11 -0.603 View CSV PDB
model_6 -0.6062 View CSV PDB
model_2 -0.607 View CSV PDB
input -0.6124 View CSV PDB
CABS_average -0.6173 View CSV PDB
model_0 -0.6331 View CSV PDB
model_8 -0.6378 View CSV PDB
model_3 -0.6605 View CSV PDB
model_4 -0.6752 View CSV PDB
model_9 -0.718 View CSV PDB