Project name: D76N/F30A [mutate: FA30A]

Status: done

Started: 2020-02-10 14:22:26
Settings
Chain sequence(s) A: MMIQRTTPKIQVYSRHPAENGKKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEEFTPTEKNEEYACRVNHVTLSQPKKIVKWDRDM
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues FA30A
Energy difference between WT (input) and mutated protein (by FoldX) 3.76714 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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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                                                       (00:00:00)
[CRITICAL]   FoldX:    FoldX encountered an error: FoldX didn't produce expected mutant file.      
                       Can't continue without it. This is unexpected and could indicate FoldX      
                       issues.                                                                     (00:00:01)
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:04)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:04)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:04)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:04)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:04)
[INFO]       FoldX:    Building mutant model                                                       (00:02:33)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:02:42)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:50)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:29:07)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:29:09)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:29:10)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:29:11)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:29:12)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:29:13)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:29:14)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:29:15)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:29:17)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:29:17)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:29:21)
[INFO]       Movie:    Creting movie with webm format                                              (00:31:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:31:21)
Show buried residues

Minimal score value
-3.4152
Maximal score value
2.1014
Average score
-0.818
Total score value
-81.8014

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
0 M A 1.7979
1 I A 2.1014
2 Q A 0.1579
3 R A -0.1291
4 T A -0.6001
5 P A -1.1968
6 K A -1.6594
7 I A -0.5213
8 Q A -0.4715
9 V A 0.0000
10 Y A -0.8427
11 S A 0.0000
12 R A -2.5076
13 H A -2.7035
14 P A -1.9997
15 A A -2.1364
16 E A -3.4152
17 N A -2.8282
18 G A -2.6543
19 K A -2.7674
20 S A -1.9778
21 N A 0.0000
22 F A -0.7553
23 L A 0.0000
24 N A -0.4038
25 C A 0.0000
26 Y A 0.1698
27 V A 0.0000
28 S A -0.1471
29 G A -0.5053
30 A A 0.0000 mutated: FA30A
31 H A -0.1323
32 P A 0.0000
33 S A -0.7168
34 D A -1.9902
35 I A -1.4332
36 E A -1.8804
37 V A 0.0000
38 D A -1.3655
39 L A 0.0000
40 L A -1.1323
41 K A -1.7184
42 N A -2.1253
43 G A -1.9039
44 E A -3.0666
45 R A -3.1472
46 I A -2.2275
47 E A -2.9440
48 K A -2.3641
49 V A -0.3252
50 E A -1.5359
51 H A -1.6104
52 S A -0.9722
53 D A -0.1125
54 L A 1.1999
55 S A 1.0726
56 F A 0.9708
57 S A -0.4957
58 K A -1.9667
59 D A -1.8692
60 W A -0.0201
61 S A 0.1476
62 F A 0.0000
63 Y A 1.0159
64 L A 0.0000
65 L A 0.3690
66 Y A 0.0000
67 Y A -0.7582
68 T A 0.0000
69 E A -0.8071
70 F A 1.1258
71 T A 0.0000
72 P A -1.1823
73 T A -1.6346
74 E A -2.8278
75 K A -3.1427
76 N A 0.0000
77 E A -2.7294
78 Y A 0.0000
79 A A 0.0000
80 C A 0.0000
81 R A -1.3873
82 V A 0.0000
83 N A -1.3366
84 H A -1.5708
85 V A 0.0000
86 T A -0.4848
87 L A 0.8408
88 S A -0.0363
89 Q A -0.4244
90 P A -0.5267
91 K A -0.3566
92 I A 1.0780
93 V A 0.0000
94 K A -1.1643
95 W A -0.1152
96 D A -1.3316
97 R A -1.6627
98 D A -1.8927
99 M A -1.1986
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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, -0.818 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_6 -0.818 View CSV PDB
model_4 -0.832 View CSV PDB
model_2 -0.859 View CSV PDB
model_5 -0.9216 View CSV PDB
model_9 -0.9735 View CSV PDB
model_1 -0.9753 View CSV PDB
model_10 -0.9985 View CSV PDB
model_8 -1.0172 View CSV PDB
model_7 -1.0221 View CSV PDB
model_0 -1.0413 View CSV PDB
model_3 -1.0555 View CSV PDB
model_11 -1.0963 View CSV PDB
input -1.1102 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018