Project name: 43c62b3b7f0f1da [mutate: TA10A]

Status: done

Started: 2020-04-05 13:54:45
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 TA10A
Energy difference between WT (input) and mutated protein (by FoldX) 0.145807 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                                        (00:00:35)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:49)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:20:09)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:20:10)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:20:10)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:20:11)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:20:11)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:20:12)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:20:12)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:20:13)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:20:13)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:20:14)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:20:15)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:20:15)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:20:16)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:20:19)
[INFO]       Movie:    Creting movie with webm format                                              (00:22:32)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:38)
Show buried residues
Minimal score value
-3.0056
Maximal score value
3.6229
Average score
-0.448
Total score value
-47.936
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 2.2048
2 T A 1.0535
3 Q A 0.0000
4 P A -0.5204
5 P A -0.6426
6 S A -0.8634
7 T A 0.0000
8 S A -0.7663
9 G A -0.7636
10 A A -0.7966 mutated: TA10A
11 P A -0.9771
12 G A -1.6828
13 Q A -2.4837
14 R A -2.6523
15 V A 0.0000
16 T A -0.5324
17 I A 0.0000
18 S A -0.3311
19 C A 0.0000
20 S A 0.0834
21 G A 0.3136
22 S A -0.0108
23 S A 0.0923
24 S A -0.7941
25 N A -0.5016
26 I A 0.5862
27 E A -1.0379
28 T A -0.8931
29 N A -1.1808
30 T A -1.2185
31 V A 0.0000
32 N A 0.3055
33 W A 0.0000
34 Y A 0.4924
35 Q A 0.0000
36 Q A -1.1692
37 L A 0.0000
38 P A -1.5376
39 G A -1.0123
40 T A -0.5015
41 A A -0.4087
42 P A -0.4671
43 K A -0.0632
44 L A 0.7466
45 V A 0.0000
46 M A 0.0000
47 H A -1.5297
48 T A -1.6666
49 N A 0.0000
50 N A -2.4266
51 Q A -2.4595
52 R A -2.0248
53 P A -0.8211
54 S A -0.2129
55 G A -0.2959
56 V A 0.7966
57 P A 0.0000
58 D A -1.6652
59 R A -1.1107
60 F A 0.1890
61 S A -0.7165
62 G A -1.0159
63 S A -1.3320
64 R A -1.7164
65 S A -1.0725
66 G A -0.9624
67 T A -0.5248
68 S A -0.6892
69 A A 0.0000
70 S A -0.7400
71 L A 0.0000
72 A A -0.1990
73 I A 0.0000
74 G A 0.0000
75 G A -0.9721
76 L A -0.5859
77 Q A 0.0000
78 S A -0.5313
79 E A -1.8559
80 D A -2.9243
81 E A -3.0056
82 A A 0.0000
83 D A -2.0377
84 Y A 0.0000
85 F A 0.2611
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.6139
90 D A -1.0234
91 D A -1.3282
92 N A -1.2217
93 L A -0.0624
94 N A -0.8541
95 G A 0.4611
96 V A 2.7748
97 I A 3.5098
98 F A 3.6229
99 G A 0.0000
100 G A 0.0322
101 G A -1.1278
102 T A 0.0000
103 K A -2.1308
104 L A 0.0000
105 T A -0.8278
106 V A -0.0194
107 L A 1.4231
Download PDB file
View in 3Dmol
Play the video

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, -0.448 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_7 -0.448 View CSV PDB
model_5 -0.465 View CSV PDB
model_0 -0.5636 View CSV PDB
model_8 -0.5783 View CSV PDB
model_1 -0.6052 View CSV PDB
model_9 -0.6059 View CSV PDB
model_11 -0.6106 View CSV PDB
model_2 -0.6238 View CSV PDB
model_4 -0.6472 View CSV PDB
input -0.6614 View CSV PDB
model_3 -0.6676 View CSV PDB
model_6 -0.6875 View CSV PDB
model_10 -0.8115 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018