Project name: 69012de7945b9a4

Status: done

Started: 2025-03-21 10:03:13
Chain sequence(s) D: TSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFAQSIISTLT
input PDB
Selected Chain(s) D
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]                                                (00:00:00)
[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 D chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:34)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:16:38)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:16:39)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:16:39)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:16:39)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:16:40)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:16:40)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:16:41)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:16:41)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:16:41)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:16:42)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:16:42)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:16:42)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:16:43)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:16:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:47)
Show buried residues
Minimal score value
-3.8518
Maximal score value
1.357
Average score
-0.8667
Total score value
-113.5326
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
3 T D -0.7294
4 S D -1.1591
5 S D -1.4904
6 S D -1.4713
7 T D -1.5383
8 K D -2.6043
9 K D -2.6672
10 T D -1.6719
11 Q D -1.3118
12 L D -0.7002
13 Q D -0.9947
14 L D 0.0000
15 E D -0.5473
16 H D -0.0915
17 L D 0.0000
18 L D 0.4007
19 L D 1.3570
20 D D 0.5151
21 L D 0.0000
22 Q D 0.1599
23 M D 0.5537
24 I D 0.0000
25 L D -0.5667
26 N D -1.4443
27 G D 0.0000
28 I D 0.0000
29 N D -2.3607
30 N D -2.7119
31 Y D 0.0000
32 K D -2.7232
33 N D -2.6905
34 P D -1.6990
35 K D -2.0604
36 L D -1.8012
37 T D -1.2862
38 R D -1.7066
39 M D 0.0000
40 L D -0.4817
41 T D -0.4916
42 F D -0.0298
43 K D -1.2184
44 F D 0.0000
45 Y D 0.0867
46 M D 0.0000
47 P D 0.0000
48 K D -1.3393
49 K D -1.7451
50 A D 0.0000
51 T D -1.1165
52 E D -1.5524
53 L D 0.0000
54 K D -1.9788
55 H D 0.0000
56 L D 0.0000
57 Q D -0.8834
58 C D 0.0000
59 L D 0.0000
60 E D -1.6614
61 E D -2.5571
62 E D -1.6533
63 L D 0.0000
64 K D -2.8627
65 P D -2.0739
66 L D 0.0000
67 E D -2.5570
68 E D -2.2625
69 V D 0.0000
70 L D 0.0000
71 N D -2.6035
72 L D -1.2059
73 A D 0.0000
74 Q D -2.4273
75 S D -1.8256
76 K D -2.6899
77 N D -2.4976
78 F D -1.9124
79 H D -2.3250
80 L D 0.0000
81 R D -3.0546
82 P D 0.0000
83 R D -3.8518
84 D D -3.3339
85 L D 0.0000
86 I D 0.0000
87 S D -1.7430
88 N D -1.3614
89 I D 0.0000
90 N D -0.8664
91 V D -0.0575
92 I D -0.3377
93 V D 0.0000
94 L D -0.4575
95 E D -1.5795
96 L D -0.9813
97 K D 0.0000
98 G D -1.3701
99 S D -1.1193
100 E D -1.5104
101 T D -0.3919
102 T D 0.0100
103 F D 0.8097
104 M D 1.2361
105 C D 0.5976
106 E D -0.5187
107 Y D 0.4805
108 A D -0.4415
109 D D -1.2539
110 E D -1.9669
111 T D -1.3215
112 A D 0.0000
113 T D -0.8173
114 I D 0.0000
115 V D -0.7528
116 E D -1.5389
117 F D 0.0000
118 L D 0.0000
119 N D -1.2967
120 R D -1.6521
121 W D 0.0000
122 I D -0.4625
123 T D -0.9767
124 F D 0.0000
125 A D 0.0000
126 Q D -1.2136
127 S D -0.6236
128 I D -0.5250
129 I D -0.1784
130 S D -0.2303
131 T D -0.0150
132 L D 0.0981
133 T D -0.0558
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, -0.8667 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_0 -0.8667 View CSV PDB
model_5 -0.8976 View CSV PDB
model_8 -0.9074 View CSV PDB
model_4 -0.9272 View CSV PDB
model_6 -0.9386 View CSV PDB
model_9 -0.9476 View CSV PDB
CABS_average -0.9578 View CSV PDB
input -0.958 View CSV PDB
model_7 -0.9599 View CSV PDB
model_10 -0.9746 View CSV PDB
model_2 -0.9862 View CSV PDB
model_1 -1.0023 View CSV PDB
model_11 -1.0339 View CSV PDB
model_3 -1.0518 View CSV PDB