Project name: 138d6c2d31981f7 [mutate: TS48A]

Status: done

Started: 2020-04-05 14:02:25
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
Mutated residues TS48A
Energy difference between WT (input) and mutated protein (by FoldX) 0.0363553 kcal/mol
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]       FoldX:    Building mutant model                                                       (00:00:42)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:44)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:02)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:27)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:27)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:28)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:28)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:29)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:29)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:30)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:32)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:32)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:33)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:33)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:34)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:35)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:39)
[INFO]       Movie:    Creting movie with webm format                                              (00:23:07)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:12)
Show buried residues
Minimal score value
-3.3888
Maximal score value
3.0706
Average score
-0.6383
Total score value
-68.2972
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 1.9145
2 T A 0.6583
3 Q A 0.0123
4 P A -0.5891
5 P A -0.8611
6 S A -1.2392
7 T A -1.0745
8 S A -0.7250
9 G A 0.0000
10 T A -0.3207
11 P A -0.5725
12 G A -1.1540
13 Q A -1.9554
14 R A -2.3356
15 V A 0.0000
16 T A -0.7049
17 I A 0.0000
18 S A -0.3961
19 C A 0.0000
20 S A -0.1184
21 G A 0.2173
22 S A 0.0000
23 S A -0.6890
24 S A -0.7708
25 N A -0.7054
26 I A 0.4036
27 E A -1.4145
28 T A -0.9668
29 N A 0.0000
30 T A -0.5083
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.6063
35 Q A 0.0000
36 Q A -0.9694
37 L A -1.2862
38 P A -1.4455
39 G A -0.9917
40 T A -0.4922
41 A A -0.3044
42 P A -0.4248
43 K A -0.3287
44 L A 0.4821
45 V A 0.0000
46 M A 0.0000
47 H A -0.9829
48 S A -1.3630 mutated: TS48A
49 N A 0.0000
50 N A -2.4327
51 Q A -2.5615
52 R A -2.1048
53 P A -1.1470
54 S A -1.0155
55 G A -0.9747
56 V A 0.0000
57 P A -1.7290
58 D A -2.5658
59 R A -2.2096
60 F A -0.9023
61 S A -0.7536
62 G A 0.0000
63 S A -1.1150
64 R A -1.5072
65 S A -0.9336
66 G A -0.9731
67 T A -0.7197
68 S A -0.3081
69 A A 0.0000
70 S A -0.4175
71 L A 0.0000
72 A A -0.3650
73 I A -0.9491
74 G A -1.6569
75 G A -1.7989
76 L A -1.5813
77 Q A -1.7886
78 S A -1.2787
79 E A 0.0000
80 D A -2.7984
81 E A -3.3888
82 A A 0.0000
83 D A -1.7521
84 Y A 0.0000
85 F A 0.5414
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A -0.3376
90 D A -2.6591
91 D A -3.1288
92 N A -2.1849
93 L A -0.1972
94 N A -1.5507
95 G A -0.5051
96 V A 1.7063
97 I A 2.4847
98 F A 3.0706
99 G A 1.7474
100 G A 0.5635
101 G A -0.5475
102 T A 0.0000
103 K A -2.4938
104 L A 0.0000
105 T A -1.6515
106 V A -0.7024
107 L A 0.6717
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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, -0.6383 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 -0.6383 View CSV PDB
model_2 -0.6462 View CSV PDB
input -0.6677 View CSV PDB
model_11 -0.6862 View CSV PDB
model_4 -0.749 View CSV PDB
model_7 -0.7524 View CSV PDB
model_1 -0.7612 View CSV PDB
model_0 -0.7638 View CSV PDB
model_6 -0.78 View CSV PDB
model_5 -0.8022 View CSV PDB
model_9 -0.8078 View CSV PDB
model_8 -0.8315 View CSV PDB
model_3 -0.8583 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018