Project name: seq2_gtp

Status: done

Started: 2025-11-05 17:19:58
Chain sequence(s) A: TEETVVVERDERRELVVKGESGVGKTSFVNSVLKGTRDHPLARAARAALEAGDFEGLKALGERYIKARGPGEVTE
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
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                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:07)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:07)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:35)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:12:36)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:12:36)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:12:37)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:12:37)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:12:37)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:12:37)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:12:37)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:12:38)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:12:38)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:12:38)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:12:38)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:12:38)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:12:39)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:12:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:42)
Show buried residues
Minimal score value
-4.6229
Maximal score value
0.6069
Average score
-1.5385
Total score value
-115.3865
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 T A -1.9507
2 E A -2.8965
3 E A -1.5944
4 T A -0.2923
5 V A 0.0000
6 V A 0.6069
7 V A 0.0000
8 E A -3.9042
9 R A -4.0458
10 D A -4.0252
11 E A -4.6229
12 R A -4.3232
13 R A -2.7339
14 E A -0.8624
15 L A 0.0000
16 V A 0.4069
17 V A 0.0000
18 K A -2.9704
19 G A -2.7084
20 E A -2.6889
21 S A -1.3604
22 G A 0.0000
23 V A -0.6476
24 G A 0.0000
25 K A -1.2989
26 T A 0.0000
27 S A -0.6453
28 F A 0.0000
29 V A 0.0000
30 N A -0.6706
31 S A 0.0000
32 V A 0.0000
33 L A 0.1508
34 K A -1.6014
35 G A -1.8372
36 T A -1.7522
37 R A -2.7411
38 D A 0.0000
39 H A -2.0088
40 P A -1.5297
41 L A 0.0000
42 A A 0.0000
43 R A -2.6159
44 A A -1.4229
45 A A 0.0000
46 R A -2.4819
47 A A -1.7813
48 A A -1.6279
49 L A -1.7042
50 E A -2.7784
51 A A -1.4986
52 G A -2.4105
53 D A -1.6922
54 F A -1.0408
55 E A -2.1425
56 G A -1.2513
57 L A 0.0000
58 K A -2.1620
59 A A -1.9306
60 L A -2.0535
61 G A 0.0000
62 E A -3.2046
63 R A -3.3572
64 Y A 0.0000
65 I A -1.9134
66 K A -3.2186
67 A A -2.7334
68 R A -2.4455
69 G A -1.6710
70 P A -1.5719
71 G A -2.1634
72 E A -2.9947
73 V A 0.0000
74 T A -2.2647
75 E A -2.7058
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, -1.5385 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 -1.5385 View CSV PDB
model_9 -1.5722 View CSV PDB
model_5 -1.59 View CSV PDB
model_0 -1.6053 View CSV PDB
model_1 -1.6373 View CSV PDB
model_4 -1.6731 View CSV PDB
CABS_average -1.6756 View CSV PDB
model_3 -1.6947 View CSV PDB
model_6 -1.7079 View CSV PDB
model_10 -1.7669 View CSV PDB
model_8 -1.7716 View CSV PDB
model_7 -1.7734 View CSV PDB
input -1.774 View CSV PDB
model_2 -1.7763 View CSV PDB