Project name: keratin

Status: done

Started: 2025-08-09 09:47:14
Chain sequence(s) A: MSCYDLCRPCGPTPLANSCNEPCVRQCQDSRVVIQPSPVVVTLPGPILSSFPQNTAVGSSTSAAVGSILSEEGVPISCGGFGISGLGSRFSGRRCLPC
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
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:20)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:08:17)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:08:17)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:08:18)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:08:18)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:08:18)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:08:18)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:08:19)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:08:19)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:08:19)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:08:19)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:08:19)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:08:20)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:08:20)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:08:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:22)
Show buried residues
Minimal score value
-2.0494
Maximal score value
2.297
Average score
0.1555
Total score value
15.2367
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 M A 1.1669
2 S A 0.2193
3 C A 0.3415
4 Y A 0.0000
5 D A 0.0000
6 L A 0.0000
7 C A 0.0000
8 R A -1.5849
9 P A -0.6237
10 C A 0.0563
11 G A -0.3780
12 P A -0.1472
13 T A -0.1288
14 P A 0.0256
15 L A 1.5104
16 A A 0.2289
17 N A -0.6980
18 S A -0.2536
19 C A 0.2681
20 N A -0.5055
21 E A -0.7775
22 P A -0.3653
23 C A 0.4579
24 V A 1.3816
25 R A 0.0000
26 Q A -0.1047
27 C A 0.5509
28 Q A -1.1086
29 D A -1.9821
30 S A -0.5470
31 R A 0.0000
32 V A 1.8377
33 V A 1.0657
34 I A 1.8973
35 Q A -0.6258
36 P A -0.4452
37 S A -0.1301
38 P A -0.0931
39 V A 1.3154
40 V A 2.2810
41 V A 2.0983
42 T A 0.5552
43 L A 1.4868
44 P A -0.0551
45 G A -0.5655
46 P A 0.0343
47 I A 2.2590
48 L A 1.8909
49 S A 0.0380
50 S A 0.1124
51 F A 1.8506
52 P A -0.1005
53 Q A -1.4915
54 N A -1.5167
55 T A -0.3024
56 A A 0.3835
57 V A 1.6953
58 G A -0.1703
59 S A -0.3508
60 S A -0.2670
61 T A -0.1713
62 S A -0.2220
63 A A -0.0133
64 A A 0.3595
65 V A 1.6879
66 G A 0.0314
67 S A 0.2053
68 I A 2.2970
69 L A 1.7354
70 S A 0.0054
71 E A -0.3986
72 E A -0.6768
73 G A -0.5918
74 V A 0.0000
75 P A 0.0590
76 I A 1.5574
77 S A 0.4047
78 C A 0.6326
79 G A -0.3401
80 G A -0.4283
81 F A 0.5427
82 G A 0.3068
83 I A 1.0494
84 S A -0.0045
85 G A -0.0284
86 L A 0.3175
87 G A -0.4193
88 S A -0.6142
89 R A -1.8286
90 F A -0.3411
91 S A -0.2247
92 G A -0.7860
93 R A -2.0494
94 R A -1.2153
95 C A 0.3526
96 L A 1.5433
97 P A 0.1784
98 C A 0.6342
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, 0.1555 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 0.1555 View CSV PDB
model_6 0.125 View CSV PDB
input 0.1104 View CSV PDB
model_8 0.066 View CSV PDB
model_4 0.0655 View CSV PDB
model_9 0.0639 View CSV PDB
CABS_average 0.0583 View CSV PDB
model_5 0.0545 View CSV PDB
model_2 0.0487 View CSV PDB
model_10 0.0376 View CSV PDB
model_7 0.0305 View CSV PDB
model_3 0.0251 View CSV PDB
model_1 0.017 View CSV PDB
model_0 0.0102 View CSV PDB