Project name: 468718088117aa1 [mutate: GS35A, AS49A, AS75A, KR87A] [mutate: AP14A, RY59A, HN84A] [mutate: YR59A]

Status: done

Started: 2026-03-06 11:06:13
Chain sequence(s) A: EVQLVESGGGLVQPGGSLRLSCAASGRTFSSYAMSWFRQAPGKEREFVSAISRSAGTTYYADSVKGRFTISRDNSKNMLYLQMNSLRPEDTAVYYCAAATLQSTVVLSTHNYDYWGQGTQVTVSS
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues YR59A
Energy difference between WT (input) and mutated protein (by FoldX) 0.816461 kcal/mol
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 A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       FoldX:    Building mutant model                                                       (00:02:34)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:40)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:29:10)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:29:12)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:29:12)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:29:13)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:29:14)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:29:14)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:29:16)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:29:17)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:29:17)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:29:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:29:23)
Show buried residues
Minimal score value
-2.4261
Maximal score value
2.0701
Average score
-0.184
Total score value
-22.9996
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 -1.8199
2 V A 0.0000
3 Q A -0.6226
4 L A 0.0000
5 V A 1.7560
6 E A 0.0000
7 S A -0.2735
8 G A -0.4425
9 G A -0.5431
10 G A 0.1265
11 L A 1.8715
12 V A 2.0701
13 Q A 0.0000
14 P A -0.0412
15 G A -0.5162
16 G A -0.3423
17 S A -0.2539
18 L A 0.0000
19 R A -1.8883
20 L A 0.0000
21 S A 0.1224
22 C A 0.0000
23 A A 0.1605
24 A A 0.0000
25 S A -0.1840
26 G A -0.4542
27 R A -1.8620
28 T A -0.3762
29 F A 0.0000
30 S A -0.2171
31 S A -0.0625
32 Y A 0.0000
33 A A 0.0000
34 M A 0.0000
35 S A 0.0000
36 W A 0.0000
37 F A 0.3668
38 R A 0.0000
39 Q A -0.8678
40 A A 0.0000
41 P A -0.2700
42 G A -0.7560
43 K A -1.7755
44 E A -2.4261
45 R A -2.2716
46 E A 0.0000
47 F A 1.6053
48 V A 0.0000
49 S A 0.0000
50 A A 0.0000
51 I A 0.0000
52 S A 0.0000
53 R A -0.4839
54 S A -0.2089
55 A A 0.0120
56 G A -0.1956
57 T A -0.1003
58 T A -0.2855
59 R A -0.9649 mutated: YR59A
60 Y A 1.1084
61 A A 0.2632
62 D A -0.2605
63 S A -0.2565
64 V A 0.0000
65 K A -1.7526
66 G A -0.8432
67 R A -1.7501
68 F A 0.0000
69 T A -0.0337
70 I A 0.0000
71 S A -0.0519
72 R A 0.0000
73 D A -1.9327
74 N A -1.1325
75 S A -0.6892
76 K A -1.7422
77 N A 0.0000
78 M A 1.0196
79 L A 0.0000
80 Y A 1.0562
81 L A 0.0000
82 Q A -0.6259
83 M A 0.0000
84 N A -0.7029
85 S A 0.0000
86 L A 0.7292
87 R A 0.0000
88 P A -0.2238
89 E A 0.0000
90 D A -1.7919
91 T A -0.3597
92 A A 0.0000
93 V A 0.2015
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 A A 0.0000
99 A A 0.0000
100 T A -0.0003
101 L A 0.1402
102 Q A -0.9918
103 S A -0.4210
104 T A -0.0510
105 V A 0.4612
106 V A 1.0373
107 L A 0.8243
108 S A 0.0871
109 T A -0.1848
110 H A -0.6874
111 N A -0.4237
112 Y A 1.0042
113 D A -1.0223
114 Y A 0.0000
115 W A 1.0195
116 G A 0.2019
117 Q A -0.3075
118 G A -0.2638
119 T A 0.0000
120 Q A -0.7845
121 V A 0.0000
122 T A -0.0569
123 V A 0.0000
124 S A -0.1593
125 S A -0.2353
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, -0.184 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 -0.184 View CSV PDB
input -0.1893 View CSV PDB
model_11 -0.2004 View CSV PDB
model_4 -0.2098 View CSV PDB
model_6 -0.2263 View CSV PDB
model_1 -0.2265 View CSV PDB
model_5 -0.2285 View CSV PDB
CABS_average -0.2288 View CSV PDB
model_2 -0.2302 View CSV PDB
model_7 -0.2304 View CSV PDB
model_10 -0.2447 View CSV PDB
model_8 -0.2485 View CSV PDB
model_0 -0.254 View CSV PDB
model_3 -0.262 View CSV PDB