Project name: Aggrescan

Status: done

Started: 2020-11-19 21:26:52
Settings
Chain sequence(s) X: PETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGGFKLTTGNA
input PDB
Selected Chain(s) X
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with X 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]       CABS:     Running CABS flex simulation                                                (00:02:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:14)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:14)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:15)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:15)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:16)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:16)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:17)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:18)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:18)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:19)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:19)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:20)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:20)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:22:21)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:22:22)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:22:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:22:23)
Show buried residues
Minimal score value
-3.9717
Maximal score value
1.1319
Average score
-1.2451
Total score value
-109.565
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
41 P X -1.4976
42 E X -2.8455
43 T X -2.5563
44 H X -2.9897
45 I X 0.0000
46 N X -1.8195
47 L X 0.0000
48 K X -0.1342
49 V X 0.0000
50 S X 0.0000
51 D X 0.0000
52 G X -1.0015
53 S X -0.8898
54 S X -1.0381
55 E X -1.4390
56 I X -0.1101
57 F X 0.8345
58 F X -0.2278
59 K X -1.8815
60 I X 0.0000
61 K X -3.0132
62 K X -2.4044
63 T X -1.3978
64 T X -1.6455
65 P X 0.0000
66 L X 0.0000
67 R X -3.9077
68 R X -3.6166
69 L X 0.0000
70 M X 0.0000
71 E X -3.9164
72 A X -2.5183
73 F X 0.0000
74 A X 0.0000
75 K X -3.9717
76 R X -3.7707
77 Q X -3.2649
78 G X -2.8358
79 K X -3.5383
80 E X -3.5441
81 M X -1.9470
82 D X -1.5654
83 S X -0.8152
84 L X 0.0000
85 R X 0.0000
86 F X 0.0000
87 L X 0.0000
88 Y X 0.0000
89 D X -2.3598
90 G X -1.6523
91 I X -1.1093
92 R X -2.1388
93 I X 0.0000
94 Q X -2.2266
95 A X -2.3968
96 D X -2.7490
97 Q X 0.0000
98 T X -1.8485
99 P X 0.0000
100 E X -3.9038
101 D X -2.8774
102 L X -2.1219
103 D X -3.1737
104 M X 0.0000
105 E X -3.4544
106 D X -3.0603
107 N X -2.2182
108 D X 0.0000
109 I X -0.0675
110 I X 0.0000
111 E X -1.0620
112 A X 0.0000
113 H X 0.0000
114 R X -2.0430
115 E X -1.6081
116 Q X -1.4269
117 I X 0.7685
118 G X -0.0307
119 G X -0.1953
120 G X 0.1462
121 F X 1.1319
122 K X -0.4988
123 L X 0.7641
124 T X -0.1313
125 T X -0.4644
126 G X -0.7579
127 N X -1.0383
128 A X -0.4916
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View in 3Dmol
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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, -1.2451 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 -1.2451 View CSV PDB
model_4 -1.2991 View CSV PDB
model_6 -1.3036 View CSV PDB
model_9 -1.3086 View CSV PDB
model_2 -1.3106 View CSV PDB
model_5 -1.3248 View CSV PDB
model_1 -1.3813 View CSV PDB
model_7 -1.3856 View CSV PDB
model_0 -1.4448 View CSV PDB
model_3 -1.4605 View CSV PDB
input -1.5208 View CSV PDB
model_10 -1.5767 View CSV PDB
model_11 -1.6166 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018