Project name: 5d472f82cf2582f [mutate: SN95A]

Status: done

Started: 2020-04-05 13:00:09
Settings
Chain sequence(s) A: QSVLTQPPSASGTPGQRVTISCSGSSSNIGSNTVNWYQQLPGTAPKLLIYSNNQRPSGVPDRFSGSKSGTSASLAISGLQSEDEADYYCAAWDDSLNGPIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues SN95A
Energy difference between WT (input) and mutated protein (by FoldX) -0.351767 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                                                       (00:01:03)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:04)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:29)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:43)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:44)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:44)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:45)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:45)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:45)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:45)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:46)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:46)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:46)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:47)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:47)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:47)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:49)
[INFO]       Movie:    Creting movie with webm format                                              (00:22:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:12)
Show buried residues

Minimal score value
-2.9772
Maximal score value
1.7867
Average score
-0.5271
Total score value
-57.9819

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 Q A -1.3406
2 S A 0.0000
3 V A -0.0773
4 L A 0.0000
5 T A 0.0575
6 Q A 0.0000
7 P A 0.0000
8 P A -0.9329
9 S A -1.1575
10 A A -0.6591
11 S A -0.3560
12 G A 0.0000
13 T A 0.0215
14 P A -0.3155
15 G A -0.7564
16 Q A -1.3719
17 R A 0.0000
18 V A -0.1966
19 T A -0.0644
20 I A 0.0000
21 S A -0.3709
22 C A 0.0000
23 S A -0.3749
24 G A -0.6370
25 S A -0.6508
26 S A -1.1181
27 S A -1.2548
28 N A 0.0000
29 I A 0.0000
30 G A -1.2773
31 S A -1.5103
32 N A -1.5432
33 T A -0.8710
34 V A 0.0000
35 N A 0.1685
36 W A 0.0000
37 Y A 1.0915
38 Q A 0.0000
39 Q A -0.7453
40 L A -1.1799
41 P A -1.3353
42 G A -1.0531
43 T A -0.4612
44 A A -0.1309
45 P A -0.0375
46 K A 0.4023
47 L A 1.6369
48 L A 0.0000
49 I A 0.0000
50 Y A 0.2035
51 S A -0.8553
52 N A -1.7300
53 N A -1.7703
54 Q A -2.1031
55 R A -1.9418
56 P A -0.5186
57 S A -0.4490
58 G A -1.1890
59 V A -0.3777
60 P A -0.9801
61 D A -1.8212
62 R A 0.0000
63 F A 0.0000
64 S A -0.5663
65 G A -0.8678
66 S A -0.7760
67 K A -1.5165
68 S A -1.0679
69 G A -0.9132
70 T A -0.7817
71 S A 0.0000
72 A A 0.0000
73 S A -0.5518
74 L A 0.0000
75 A A -0.0512
76 I A 0.0000
77 S A -0.9260
78 G A -0.7471
79 L A 0.2746
80 Q A -1.0477
81 S A -0.7160
82 E A 0.0000
83 D A -2.5852
84 E A -2.7588
85 A A 0.0000
86 D A -1.6458
87 Y A 0.0000
88 Y A 0.2374
89 C A 0.0000
90 A A 0.3668
91 A A 0.0000
92 W A 0.0000
93 D A -2.9772
94 D A -2.9257
95 N A -1.5598 mutated: SN95A
96 L A -0.4221
97 N A -1.4036
98 G A -0.4267
99 P A 0.6508
100 I A 1.7867
101 F A 1.3144
102 G A 0.1713
103 G A -0.6034
104 G A -0.4896
105 T A 0.0000
106 K A -2.2533
107 L A 0.0000
108 T A -1.0224
109 V A -0.2939
110 L A 1.0469
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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, -0.5271 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_4 -0.5271 View CSV PDB
model_8 -0.5376 View CSV PDB
model_7 -0.5544 View CSV PDB
model_6 -0.5965 View CSV PDB
model_1 -0.6156 View CSV PDB
model_3 -0.6208 View CSV PDB
model_11 -0.621 View CSV PDB
model_0 -0.6276 View CSV PDB
model_5 -0.6661 View CSV PDB
model_10 -0.6696 View CSV PDB
model_2 -0.6757 View CSV PDB
input -0.7418 View CSV PDB
model_9 -0.7651 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018