Project name: 294

Status: done

Started: 2025-12-11 11:49:25
Chain sequence(s) H: EVQLVESGGGLVQAGESLKLSCAASGRPFSTYTMGWFRQAPGKEREIVAASNWSGGSKYYSDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCATRESGELRIREYEYDYWGQGTQVTVSS
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with H chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:21)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:16:49)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:16:50)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:16:50)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:16:50)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:16:50)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:16:51)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:16:51)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:16:51)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:16:52)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:16:52)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:16:52)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:16:53)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:16:53)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:16:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:55)
Show buried residues
Minimal score value
-2.9496
Maximal score value
1.1088
Average score
-0.7841
Total score value
-97.2283
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 -2.3188
2 V H 0.0000
3 Q H -1.5628
4 L H 0.0000
5 V H 0.6947
6 E H -0.4342
7 S H -0.6869
8 G H -1.0076
9 G H -0.7739
11 G H -0.2540
12 L H 0.6572
13 V H 0.0000
14 Q H -1.1604
15 A H -0.8841
16 G H -1.1286
17 E H -1.7104
18 S H -1.3226
19 L H 0.0000
20 K H -1.4103
21 L H 0.0000
22 S H -0.2560
23 C H 0.0000
24 A H -0.1809
25 A H -1.1110
26 S H -1.4145
27 G H -1.7476
28 R H -2.7578
29 P H -2.0193
30 F H 0.0000
35 S H -1.1117
36 T H -0.3634
37 Y H -0.5617
38 T 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 -1.3086
45 A H -1.2637
46 P H -1.4871
47 G H -1.9900
48 K H -2.9014
49 E H -2.8844
50 R H -1.8192
51 E H 0.0000
52 I H 0.0000
53 V H 0.0000
54 A H 0.0000
55 A H 0.0000
56 S H 0.0000
57 N H -0.5188
58 W H -0.0311
59 S H -0.1806
62 G H -0.6642
63 G H -0.7444
64 S H -0.3222
65 K H -0.4759
66 Y H 0.9782
67 Y H 1.1088
68 S H -0.2477
69 D H -0.8260
70 S H -0.6172
71 V H -0.6879
72 K H -0.8751
74 G H -1.3005
75 R H -1.6909
76 F H -0.5561
77 T H -0.1187
78 I H 0.0000
79 S H -0.5213
80 R H -1.2402
81 D H -2.4442
82 N H -2.5022
83 A H -1.9474
84 K H -2.6153
85 N H -2.3315
86 T H 0.0000
87 V H 0.0000
88 Y H 0.0003
89 L H 0.0000
90 Q H -1.0353
91 M H 0.0000
92 N H -1.6854
93 S H 0.0000
94 L H 0.0000
95 K H -2.5765
96 P H -2.4408
97 E H -2.9496
98 D H -2.5563
99 T H -1.3338
100 A H 0.0000
101 V H -0.3621
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 T H 0.0000
107 R H 0.0000
108 E H -2.4277
109 S H -1.6542
110 G H -1.0710
111 E H 0.0000
111A L H 0.0775
111B R H -1.8139
112B I H -1.7129
112A R H -2.5824
112 E H -1.9671
113 Y H 0.0000
114 E H -2.6089
115 Y H -1.4508
116 D H -1.4384
117 Y H -0.2735
118 W H 0.5310
119 G H -0.1108
120 Q H -0.2527
121 G H -0.4862
122 T H 0.0000
123 Q H -0.9386
124 V H 0.0000
125 T H -0.4503
126 V H 0.0000
127 S H -1.0141
128 S H -0.7904
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, -0.7841 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_0 -0.7841 View CSV PDB
input -0.8092 View CSV PDB
model_11 -0.8346 View CSV PDB
model_9 -0.877 View CSV PDB
model_4 -0.8854 View CSV PDB
model_2 -0.8934 View CSV PDB
CABS_average -0.9202 View CSV PDB
model_6 -0.9375 View CSV PDB
model_1 -0.9391 View CSV PDB
model_7 -0.9578 View CSV PDB
model_5 -0.9642 View CSV PDB
model_10 -0.9696 View CSV PDB
model_8 -0.9978 View CSV PDB
model_3 -1.0016 View CSV PDB