Project name: 1BMZ [mutate: LP55A]

Status: done

Started: 2026-02-11 09:16:03
Chain sequence(s) A: GPTGTGESKCPLMVKVLDAVRGSPAINVAVHVFRKAADDTWEPFASGKTSESGELHGLTTEEEFVEGIYKVEIDTKSYWKALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode Yes
Automated mutations No
Mutated residues LP55A
Energy difference between WT (input) and mutated protein (by FoldX) 6.75026 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:33)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:33)
[INFO]       FoldX:    Building mutant model                                                       (00:01:48)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:51)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:19:01)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:19:01)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:19:02)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:19:03)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:19:04)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:19:04)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:19:04)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:19:05)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:19:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:19:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:19:10)
Show buried residues
Minimal score value
-3.0028
Maximal score value
1.5956
Average score
-0.601
Total score value
-76.3245
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 G A -0.5150
2 P A -0.4753
3 T A -0.4271
4 G A 0.0000
5 T A -0.5753
6 G A -0.9669
7 E A -1.2648
8 S A -1.1608
9 K A -0.6753
10 C A -0.3572
11 P A -0.6838
12 L A 0.0000
13 M A 0.0000
14 V A 0.0000
15 K A -0.7438
16 V A 0.0000
17 L A 0.1924
18 D A 0.0000
19 A A -0.1341
20 V A -0.3024
21 R A -1.6141
22 G A -1.0547
23 S A -0.6523
24 P A -0.6316
25 A A 0.0000
26 I A -0.1885
27 N A -1.4062
28 V A 0.0000
29 A A -1.6417
30 V A 0.0000
31 H A -0.7998
32 V A 0.0000
33 F A 0.7588
34 R A 0.0000
35 K A -1.0683
36 A A -0.9793
37 A A -1.5303
38 D A -2.4398
39 D A -2.3316
40 T A -1.1717
41 W A 0.2584
42 E A -0.0291
43 P A 0.4280
44 F A 1.5956
45 A A 0.4473
46 S A -0.3428
47 G A -1.1765
48 K A -2.2775
49 T A 0.0000
50 S A -1.5169
51 E A 0.0000
52 S A -0.9060
53 G A -1.4348
54 E A -2.2472
55 P A -1.6054 mutated: LP55A
56 H A 0.0000
57 G A -0.7981
58 L A -0.0444
59 T A 0.1890
60 T A -0.5122
61 E A 0.0000
62 E A -2.5654
63 E A -2.2381
64 F A -1.0708
65 V A -0.3638
66 E A -1.4016
67 G A -0.2956
68 I A 0.7610
69 Y A 0.0000
70 K A -0.5096
71 V A 0.0000
72 E A -1.4091
73 I A 0.0000
74 D A -2.2164
75 T A 0.0000
76 K A -2.4046
77 S A -1.6450
78 Y A 0.0000
79 W A 0.0000
80 K A -1.8850
81 A A -0.8389
82 L A -0.5527
83 G A 0.0579
84 I A 0.6187
85 S A -0.3979
86 P A 0.3430
87 F A 1.4897
88 H A -0.1838
89 E A -1.5892
90 H A -2.0855
91 A A 0.0000
92 E A -2.1698
93 V A -0.3959
94 V A 1.2538
95 F A 0.0000
96 T A 0.0736
97 A A 0.0000
98 N A -1.2299
99 D A -1.6339
100 S A -1.1082
101 G A -1.9860
102 P A -2.4180
103 R A -2.2499
104 R A -1.3004
105 Y A 0.0000
106 T A 0.0000
107 I A 0.0000
108 A A 0.0000
109 A A 0.0000
110 L A 0.5860
111 L A 0.0000
112 S A 0.2131
113 P A 0.3526
114 Y A 0.0000
115 S A 0.3738
116 Y A 0.4315
117 S A 0.0450
118 T A 0.0538
119 T A 0.0028
120 A A 0.1982
121 V A 0.0632
122 V A -0.0039
123 T A 0.0000
124 N A -2.0020
125 P A -2.3793
126 K A -2.8961
127 E A -3.0028
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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, -0.601 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_11 -0.601 View CSV PDB
model_6 -0.6059 View CSV PDB
model_5 -0.6159 View CSV PDB
model_3 -0.6215 View CSV PDB
model_0 -0.6245 View CSV PDB
model_10 -0.6303 View CSV PDB
model_8 -0.6442 View CSV PDB
model_4 -0.6496 View CSV PDB
CABS_average -0.666 View CSV PDB
model_7 -0.6833 View CSV PDB
input -0.7004 View CSV PDB
model_9 -0.7355 View CSV PDB
model_1 -0.7459 View CSV PDB
model_2 -0.8339 View CSV PDB