Project name: b2cde7530d30f61 [mutate: FY85A]

Status: done

Started: 2020-04-05 14:03:59
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 FY85A
Energy difference between WT (input) and mutated protein (by FoldX) -0.299505 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                                                       (00:00:39)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:25)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:46)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:44)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:45)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:45)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:45)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:45)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:46)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:46)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:47)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:47)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:48)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:48)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:48)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:49)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:50)
[INFO]       Movie:    Creting movie with webm format                                              (00:23:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:28)
Show buried residues
Minimal score value
-2.6885
Maximal score value
2.8927
Average score
-0.581
Total score value
-62.1667
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 0.7344
2 T A -0.2423
3 Q A -0.6275
4 P A -0.6943
5 P A -1.0154
6 S A -0.9862
7 T A 0.0000
8 S A -0.8465
9 G A -0.9020
10 T A -0.5626
11 P A -0.9969
12 G A -1.6024
13 Q A -2.5301
14 R A -2.6885
15 V A 0.0000
16 T A -0.9783
17 I A 0.0000
18 S A -0.4569
19 C A 0.0000
20 S A -0.3817
21 G A -0.0591
22 S A -0.3426
23 S A -0.0084
24 S A -0.8101
25 N A -0.5150
26 I A 0.6922
27 E A -1.2468
28 T A -1.2539
29 N A -1.4597
30 T A 0.0000
31 V A 0.0000
32 N A 0.5553
33 W A 0.0000
34 Y A 0.2131
35 Q A 0.0000
36 Q A -0.9598
37 L A -1.2407
38 P A -1.0874
39 G A -1.0267
40 T A -0.7464
41 A A -0.6702
42 P A -0.7679
43 K A -0.8120
44 L A 0.5504
45 V A 0.0000
46 M A 0.0000
47 H A -1.2338
48 T A -1.4998
49 N A -2.2702
50 N A -2.4776
51 Q A -2.2810
52 R A -2.5833
53 P A -1.2883
54 S A -0.9565
55 G A -0.2967
56 V A 0.8557
57 P A -0.7337
58 D A -1.7767
59 R A -1.2785
60 F A -0.7183
61 S A -0.6623
62 G A -1.0088
63 S A -1.1314
64 R A -1.8433
65 S A -1.1722
66 G A -0.9157
67 T A -0.6996
68 S A -0.8257
69 A A 0.0000
70 S A -0.6904
71 L A 0.0000
72 A A -0.5521
73 I A 0.0000
74 G A -1.5420
75 G A -1.3619
76 L A -1.0138
77 Q A -1.5096
78 S A -0.9270
79 E A 0.0000
80 D A -2.1783
81 E A -2.0458
82 A A 0.0000
83 D A -1.3270
84 Y A 0.0000
85 Y A 0.2075 mutated: FY85A
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.4375
90 D A -0.8607
91 D A -1.1135
92 N A -1.2202
93 L A 0.1035
94 N A -0.6029
95 G A 0.4315
96 V A 2.2009
97 I A 2.8927
98 F A 2.3288
99 G A 0.7136
100 G A -0.3254
101 G A -1.0667
102 T A 0.0000
103 K A -1.7736
104 L A 0.0000
105 T A -0.3419
106 V A 0.1624
107 L A 1.3783
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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, -0.581 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_2 -0.581 View CSV PDB
model_4 -0.5952 View CSV PDB
model_11 -0.6046 View CSV PDB
model_3 -0.6133 View CSV PDB
model_0 -0.6187 View CSV PDB
model_1 -0.6498 View CSV PDB
input -0.6604 View CSV PDB
model_7 -0.6643 View CSV PDB
model_10 -0.6646 View CSV PDB
model_9 -0.6875 View CSV PDB
model_5 -0.7099 View CSV PDB
model_6 -0.7171 View CSV PDB
model_8 -0.7561 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018