Project name: JPG4

Status: done

Started: 2024-05-08 09:48:15
Chain sequence(s) A: MGIRMNKTVAVRTLDPERLGREGVQKEDIPPADLSDQVPDTESETRILLQGTPVAQDHQELNLDVSLQLPSRSSKITHRIHWESASLLRSEETKENEGFTVTAEGKGQGTLSVVTMYHAKASGENLYFQSSGHHHHHH
input PDB
Selected Chain(s) A
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]                                                (00:00:10)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:10)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:10)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:10)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:10)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:02)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:21:54)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:21:54)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:21:55)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:21:55)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:21:55)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:21:56)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:21:56)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:21:57)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:21:57)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:21:58)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:21:58)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:21:59)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:21:59)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:22:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:05)
Show buried residues
Minimal score value
-3.4864
Maximal score value
1.8278
Average score
-0.8734
Total score value
-120.5267
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 0.4211
2 G A -0.6588
3 I A -0.9102
4 R A -1.8448
5 M A -1.2760
6 N A -1.3694
7 K A 0.0000
8 T A -0.7640
9 V A 0.0000
10 A A -0.3349
11 V A 0.9850
12 R A -0.2025
13 T A -0.0645
14 L A 0.0000
15 D A 0.0000
16 P A 0.0000
17 E A -3.0716
18 R A -2.2248
19 L A -0.3908
20 G A -1.7393
21 R A -3.0093
22 E A -3.2334
23 G A -2.0968
24 V A -1.5443
25 Q A 0.0000
26 K A -2.1537
27 E A 0.0000
28 D A -2.1632
29 I A 0.0000
30 P A -0.5552
31 P A -0.3568
32 A A -0.0849
33 D A -0.2076
34 L A 0.8064
35 S A -0.7655
36 D A -2.3168
37 Q A -2.2050
38 V A -1.4716
39 P A -1.5803
40 D A -2.3978
41 T A -2.1128
42 E A -2.0586
43 S A 0.0000
44 E A -2.1397
45 T A 0.0000
46 R A -1.7048
47 I A 0.0000
48 L A -0.0117
49 L A 0.0000
50 Q A 0.1782
51 G A 0.0000
52 T A 0.3626
53 P A 0.3262
54 V A 1.0106
55 A A -0.3474
56 Q A -1.5288
57 D A -2.8120
58 H A -2.5327
59 Q A -2.1304
60 E A -2.7755
61 L A 0.0000
62 N A -2.7080
63 L A 0.0000
64 D A -1.9642
65 V A 0.0000
66 S A -1.0932
67 L A 0.0000
68 Q A -1.1059
69 L A -0.9429
70 P A -0.8949
71 S A -1.3916
72 R A -2.3662
73 S A -1.4964
74 S A -1.4106
75 K A -1.6923
76 I A -0.6068
77 T A -0.9562
78 H A -1.4973
79 R A -2.5164
80 I A 0.0000
81 H A 0.0000
82 W A -0.9047
83 E A -2.2182
84 S A -1.2211
85 A A -0.0224
86 S A 0.4245
87 L A 1.8278
88 L A 1.6234
89 R A -0.1794
90 S A -0.6837
91 E A -1.5558
92 E A -2.9340
93 T A 0.0000
94 K A -3.4864
95 E A -3.3541
96 N A -2.2476
97 E A 0.0000
98 G A -0.3663
99 F A -0.1594
100 T A -1.0791
101 V A 0.0000
102 T A -1.1045
103 A A 0.0000
104 E A -2.1400
105 G A -1.9959
106 K A -2.8589
107 G A 0.0000
108 Q A 0.0000
109 G A 0.0000
110 T A 0.1059
111 L A 0.0000
112 S A 0.5539
113 V A 0.0000
114 V A -0.3981
115 T A 0.0000
116 M A -0.9833
117 Y A 0.0000
118 H A -1.5885
119 A A 0.0000
120 K A -2.3636
121 A A -1.5733
122 S A -1.3428
123 G A -0.4627
124 E A -1.2714
125 N A -0.8065
126 L A 0.4749
127 Y A 1.6413
128 F A 1.5083
129 Q A -0.0764
130 S A 0.4107
131 S A 0.2143
132 G A -0.4959
133 H A -1.0624
134 H A -1.5931
135 H A -1.9774
136 H A -1.9044
137 H A -1.7238
138 H A -1.4756
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, -0.8734 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_3 -0.8734 View CSV PDB
model_9 -0.9284 View CSV PDB
model_8 -0.937 View CSV PDB
model_0 -0.9372 View CSV PDB
model_2 -0.9657 View CSV PDB
CABS_average -1.0174 View CSV PDB
model_4 -1.0334 View CSV PDB
model_1 -1.0342 View CSV PDB
model_5 -1.0555 View CSV PDB
model_7 -1.0577 View CSV PDB
model_10 -1.0924 View CSV PDB
model_11 -1.1124 View CSV PDB
model_6 -1.1815 View CSV PDB
input -1.2243 View CSV PDB