Project name: ea613c62b24bc7c [mutate: RK64A]

Status: done

Started: 2020-04-05 14:41:00
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 RK64A
Energy difference between WT (input) and mutated protein (by FoldX) -1.99942 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                                                       (00:00:34)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:40)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:55)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:15:17)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:15:17)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:15:18)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:15:18)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:15:18)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:15:19)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:15:19)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:15:19)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:15:20)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:15:20)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:15:20)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:15:21)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:15:21)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:15:23)
[INFO]       Movie:    Creting movie with webm format                                              (00:16:39)
[INFO]       Main:     Simulation completed successfully.                                          (00:16:41)
Show buried residues
Minimal score value
-3.1703
Maximal score value
3.4615
Average score
-0.4869
Total score value
-52.0951
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 2.4067
2 T A 0.8994
3 Q A 0.0000
4 P A -0.5739
5 P A -0.7696
6 S A -1.1319
7 T A -0.5708
8 S A -0.0986
9 G A 0.2721
10 T A 0.0000
11 P A -0.5695
12 G A -1.1365
13 Q A -1.6328
14 R A -2.2825
15 V A 0.0000
16 T A -0.9004
17 I A 0.0000
18 S A -0.3553
19 C A 0.0000
20 S A -0.1239
21 G A 0.3430
22 S A -0.4312
23 S A -0.5071
24 S A -0.5652
25 N A -0.9035
26 I A 0.7275
27 E A -0.7396
28 T A -0.7868
29 N A 0.0000
30 T A -0.4317
31 V A 0.0000
32 N A 0.0905
33 W A 0.0000
34 Y A 0.7120
35 Q A 0.0000
36 Q A -0.6425
37 L A -0.9181
38 P A -1.0650
39 G A -0.5383
40 T A -0.3885
41 A A -0.1314
42 P A -0.1624
43 K A -0.1576
44 L A 0.6718
45 V A 0.0000
46 M A 0.0000
47 H A -1.6272
48 T A 0.0000
49 N A -2.1802
50 N A -2.7241
51 Q A -3.1334
52 R A -3.1703
53 P A -2.2775
54 S A -1.3967
55 G A -0.9813
56 V A -1.1661
57 P A -1.6621
58 D A -2.9496
59 R A -3.0036
60 F A 0.0000
61 S A -1.2337
62 G A 0.0000
63 S A -1.3813
64 K A -1.2445 mutated: RK64A
65 S A -0.7931
66 G A -0.9646
67 T A 0.0000
68 S A -0.5253
69 A A 0.0000
70 S A -0.4085
71 L A 0.0000
72 A A -0.8999
73 I A 0.0000
74 G A -2.0178
75 G A -1.9828
76 L A -1.8762
77 Q A -1.6267
78 S A -1.1149
79 E A 0.0000
80 D A -2.5548
81 E A -2.6086
82 A A 0.0000
83 D A -1.6265
84 Y A 0.0000
85 F A 0.5078
86 C A 0.0000
87 A A 2.1991
88 A A 0.0000
89 W A 1.5709
90 D A -0.2673
91 D A -1.6804
92 N A -1.5036
93 L A 0.0995
94 N A -0.9238
95 G A 0.4879
96 V A 2.8764
97 I A 3.4615
98 F A 3.3405
99 G A 1.2898
100 G A -0.2941
101 G A -1.0439
102 T A 0.0000
103 K A -2.6843
104 L A 0.0000
105 T A -0.7386
106 V A 0.8532
107 L A 1.8772
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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, -0.4869 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_9 -0.4869 View CSV PDB
model_2 -0.5881 View CSV PDB
model_11 -0.5935 View CSV PDB
model_8 -0.6137 View CSV PDB
model_7 -0.6186 View CSV PDB
model_5 -0.6313 View CSV PDB
model_6 -0.6559 View CSV PDB
input -0.6616 View CSV PDB
model_1 -0.6678 View CSV PDB
model_3 -0.6772 View CSV PDB
model_0 -0.6919 View CSV PDB
model_4 -0.7006 View CSV PDB
model_10 -0.7833 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018