Project name: 3e5633b51600c48

Status: done

Started: 2020-04-05 13:54:29
Settings
Chain sequence(s) A: LTQPPSTSGTPGQRVTISCSGSSSNIETNTVNWYQQLPGTAPKLVMHTNNQRPSGVPDRFSGSRSGTSASLAIGGLQSEDEADYFCAAWDDNLNGVIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
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 minimalization                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:34)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:19:16)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:19:17)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:19:18)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:19:19)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:19:19)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:19:20)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:19:20)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:19:21)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:19:21)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:19:22)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:19:22)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:19:27)
[INFO]       Movie:    Creting movie with webm format                                              (00:21:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:48)
Show buried residues
Minimal score value
-2.8098
Maximal score value
3.1131
Average score
-0.5441
Total score value
-58.2201
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 L A 2.4409
2 T A 0.8976
3 Q A 0.0370
4 P A 0.0000
5 P A -0.8747
6 S A -1.0721
7 T A -1.0042
8 S A -0.6259
9 G A -0.4799
10 T A -0.6374
11 P A -0.8908
12 G A -1.6431
13 Q A -1.9875
14 R A -2.6367
15 V A 0.0000
16 T A -0.7762
17 I A 0.0000
18 S A -0.4093
19 C A 0.0000
20 S A -0.0698
21 G A 0.6986
22 S A 0.3514
23 S A -0.5373
24 S A -0.9307
25 N A -0.9928
26 I A 0.7433
27 E A -0.2265
28 T A -0.5508
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.5789
35 Q A 0.0000
36 Q A -0.8275
37 L A -1.2859
38 P A -1.0777
39 G A -0.8815
40 T A -0.5159
41 A A -0.4093
42 P A -0.5267
43 K A -0.4917
44 L A 0.2288
45 V A 0.0000
46 M A 0.0000
47 H A -1.5671
48 T A -1.7138
49 N A -2.1568
50 N A -2.5451
51 Q A -2.8098
52 R A -1.8677
53 P A -1.2106
54 S A -0.9366
55 G A -1.2125
56 V A 0.0000
57 P A -1.7713
58 D A -2.5444
59 R A -2.2274
60 F A 0.0000
61 S A -0.8879
62 G A -1.3087
63 S A -1.2654
64 R A -1.8482
65 S A -1.1430
66 G A -1.2145
67 T A -0.6584
68 S A -0.8276
69 A A 0.0000
70 S A -0.6612
71 L A 0.0000
72 A A -0.7153
73 I A 0.0000
74 G A -2.0315
75 G A 0.0000
76 L A -1.5161
77 Q A -1.7440
78 S A -1.0499
79 E A 0.0000
80 D A -2.0671
81 E A -2.0508
82 A A 0.0000
83 D A -1.3248
84 Y A 0.0000
85 F A 0.7801
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.6176
90 D A -0.6761
91 D A -1.2277
92 N A -1.1524
93 L A 0.0243
94 N A -0.9761
95 G A -0.2429
96 V A 1.5826
97 I A 2.5747
98 F A 3.1131
99 G A 1.6503
100 G A 0.1888
101 G A -1.0618
102 T A 0.0000
103 K A -1.9295
104 L A 0.0000
105 T A -0.7808
106 V A -0.3818
107 L A 0.9404
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.5441 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 A3D Score
model_10 -0.5441 View CSV PDB
model_6 -0.5558 View CSV PDB
model_1 -0.5734 View CSV PDB
model_8 -0.5758 View CSV PDB
model_11 -0.5795 View CSV PDB
model_4 -0.6123 View CSV PDB
model_9 -0.6183 View CSV PDB
model_5 -0.6367 View CSV PDB
input -0.6701 View CSV PDB
model_7 -0.6868 View CSV PDB
model_0 -0.6912 View CSV PDB
model_2 -0.7298 View CSV PDB
model_3 -0.7577 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018