Project name: 91e48fdca7f00 [mutate: HY47A]

Status: done

Started: 2020-04-05 14:01:58
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 HY47A
Energy difference between WT (input) and mutated protein (by FoldX) -1.07844 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             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:00:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:42)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:01)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:57)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:57)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:58)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:58)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:58)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:59)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:59)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:59)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:23:00)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:23:00)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:23:01)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:23:01)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:23:02)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:23:04)
[INFO]       Movie:    Creting movie with webm format                                              (00:24:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:46)
Show buried residues
Minimal score value
-2.9191
Maximal score value
3.3202
Average score
-0.2917
Total score value
-31.2095
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 2.0148
2 T A 0.8227
3 Q A -0.1333
4 P A -0.7986
5 P A -0.9884
6 S A -1.2195
7 T A -0.6553
8 S A -0.4149
9 G A 0.0018
10 T A -0.0566
11 P A -0.3154
12 G A -0.7821
13 Q A -1.0585
14 R A -0.2049
15 V A 0.1665
16 T A 0.1909
17 I A 0.0000
18 S A -0.2528
19 C A 0.0000
20 S A -0.0999
21 G A 0.0896
22 S A 0.1905
23 S A -0.4934
24 S A -0.2410
25 N A -0.1873
26 I A 0.7195
27 E A -1.0706
28 T A -0.7569
29 N A -0.9869
30 T A -0.9303
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.5176
35 Q A 0.0000
36 Q A -1.0263
37 L A -0.8790
38 P A -1.0571
39 G A -0.7029
40 T A -0.3528
41 A A -0.2303
42 P A -0.3034
43 K A 0.0827
44 L A 0.4586
45 V A 0.0000
46 M A 0.0000
47 Y A -0.0821 mutated: HY47A
48 T A -0.7423
49 N A 0.0000
50 N A -2.0240
51 Q A -1.8881
52 R A -1.3182
53 P A -0.6183
54 S A -0.5073
55 G A -0.1850
56 V A 0.6654
57 P A 0.0000
58 D A -1.2460
59 R A -0.6318
60 F A 0.0451
61 S A -0.5002
62 G A -0.9072
63 S A -1.1293
64 R A -0.7961
65 S A -0.3000
66 G A 0.0000
67 T A -0.1390
68 S A -0.3524
69 A A 0.0000
70 S A -0.4580
71 L A 0.0000
72 A A 0.2383
73 I A 0.0000
74 G A -0.1371
75 G A 0.0000
76 L A 0.8107
77 Q A 0.0000
78 S A -0.4198
79 E A -1.2364
80 D A 0.0000
81 E A -2.5870
82 A A 0.0000
83 D A -1.6704
84 Y A 0.0000
85 F A 0.1305
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A -0.4895
90 D A -2.4135
91 D A -2.9191
92 N A -1.5918
93 L A 0.2526
94 N A -1.5445
95 G A -0.3547
96 V A 1.8878
97 I A 3.2727
98 F A 3.3202
99 G A 0.0000
100 G A 0.3476
101 G A -0.7541
102 T A 0.0000
103 K A -2.5556
104 L A 0.0000
105 T A -0.6828
106 V A 0.4211
107 L A 1.5233
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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, -0.2917 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_8 -0.2917 View CSV PDB
model_2 -0.3229 View CSV PDB
model_10 -0.3337 View CSV PDB
model_1 -0.3391 View CSV PDB
model_9 -0.3565 View CSV PDB
model_3 -0.3685 View CSV PDB
model_4 -0.3923 View CSV PDB
model_7 -0.3938 View CSV PDB
model_5 -0.4002 View CSV PDB
model_0 -0.4049 View CSV PDB
model_6 -0.476 View CSV PDB
model_11 -0.5256 View CSV PDB
input -0.6257 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018