Project name: 1106

Status: done

Started: 2025-12-11 12:03:29
Chain sequence(s) H: DVQLQESGGGLVQAGGSLRLSCAASGNTMSNYRMAWFRQAPGKEREGVAIIWGNGYTKYADSVKGRFTISQDNAKRTLYLQMNSLKPEDTAMYYCAADSSDAWAGPFSPGRYNYWGQGTQVTVSS
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with H chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:03)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:36)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:31:21)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:31:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:31:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:31:23)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:31:24)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:31:24)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:31:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:31:25)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:31:26)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:31:27)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:31:27)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:31:28)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:31:29)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:31:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:31:34)
Show buried residues
Minimal score value
-3.0812
Maximal score value
1.4059
Average score
-0.6816
Total score value
-85.197
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 D H -2.3420
2 V H 0.0000
3 Q H -2.0246
4 L H 0.0000
5 Q H -2.0250
6 E H -1.6168
7 S H -1.4406
8 G H -1.5372
9 G H -0.7540
11 G H 0.0000
12 L H 1.4059
13 V H 0.7778
14 Q H -0.4592
15 A H -0.5010
16 G H -0.8059
17 G H -0.8475
18 S H -1.3064
19 L H 0.0000
20 R H -2.4194
21 L H 0.0000
22 S H -0.8489
23 C H 0.0000
24 A H -1.0839
25 A H 0.0000
26 S H -1.5949
27 G H -1.3855
28 N H -1.6281
29 T H -1.4523
30 M H 0.0000
35 S H -1.5100
36 N H -1.3626
37 Y H 0.0000
38 R H 0.0000
39 M H 0.0000
40 A H 0.0000
41 W H 0.0000
42 F H 0.0000
43 R H 0.0000
44 Q H -1.4115
45 A H 0.0000
46 P H -1.5245
47 G H -1.9205
48 K H -2.6015
49 E H -3.0812
50 R H -2.5938
51 E H 0.0000
52 G H 0.0000
53 V H 0.0000
54 A H 0.0000
55 I H 0.0000
56 I H 0.3656
57 W H 0.0000
58 G H -0.7881
59 N H -0.6508
63 G H -0.3749
64 Y H 0.6009
65 T H 0.1724
66 K H -0.1936
67 Y H -0.0189
68 A H -0.2527
69 D H -0.3686
70 S H 0.0000
71 V H -0.0706
72 K H -1.5501
74 G H 0.0000
75 R H -1.8222
76 F H 0.0000
77 T H -0.6053
78 I H 0.0770
79 S H -0.3828
80 Q H -1.2297
81 D H -1.9710
82 N H -2.4433
83 A H -1.7549
84 K H -2.6073
85 R H -2.4115
86 T H -1.4502
87 L H 0.0000
88 Y H -0.4485
89 L H 0.0000
90 Q H -1.6737
91 M H 0.0000
92 N H -1.8258
93 S H -1.3544
94 L H 0.0000
95 K H -1.8066
96 P H -1.5079
97 E H -2.4955
98 D H 0.0000
99 T H -0.6673
100 A H 0.0000
101 M H -0.1353
102 Y H 0.0000
103 Y H -0.4915
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 D H 0.0000
108 S H -1.0488
109 S H -0.9528
110 D H -1.1969
111 A H -0.3869
111A W H 0.1287
111B A H 0.1911
111C G H -0.0006
112C P H -0.1089
112B F H 0.2833
112A S H 0.0000
112 P H -0.5278
113 G H -1.1479
114 R H -1.6621
115 Y H -0.4136
116 N H -1.3070
117 Y H -0.6527
118 W H -0.4052
119 G H 0.0000
120 Q H -1.6858
121 G H -1.4177
122 T H 0.0000
123 Q H -0.5329
124 V H 0.0000
125 T H 0.2406
126 V H 0.0000
127 S H -0.4853
128 S H -0.0756
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, -0.6816 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_9 -0.6816 View CSV PDB
model_4 -0.8345 View CSV PDB
model_2 -0.8418 View CSV PDB
model_10 -0.85 View CSV PDB
CABS_average -0.9268 View CSV PDB
model_8 -0.9324 View CSV PDB
model_0 -0.9356 View CSV PDB
model_5 -0.9523 View CSV PDB
model_11 -0.9678 View CSV PDB
input -0.9882 View CSV PDB
model_7 -1.0013 View CSV PDB
model_6 -1.0219 View CSV PDB
model_1 -1.0365 View CSV PDB
model_3 -1.0654 View CSV PDB