Project name: SP1_40 [mutate: FT29A, FT31A, AL30A, IV34A]

Status: done

Started: 2020-02-12 20:06:51
Settings
Chain sequence(s) A: LRRFSTAPFAFIDINDVINF
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues FT29A,FT31A,AL30A,IV34A
Energy difference between WT (input) and mutated protein (by FoldX) -0.574699 kcal/mol
Downloads Download all the data
Simulation log
[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                                                       (00:00:20)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:29)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:35)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:05:12)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:05:13)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:05:15)
[INFO]       Movie:    Creting movie with webm format                                              (00:06:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:24)
Show buried residues

Minimal score value
-1.536
Maximal score value
3.8053
Average score
1.2042
Total score value
24.0845

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
21 L A 1.1906
22 R A -1.5360
23 R A -1.0446
24 F A 1.1272
25 S A 0.7007
26 T A 0.7882
27 A A 0.7804
28 P A 0.4665
29 T A 1.4554 mutated: FT29A
30 L A 2.6333 mutated: AL30A
31 T A 2.5362 mutated: FT31A
32 I A 2.9902
33 D A 0.6340
34 V A 1.4143 mutated: IV34A
35 N A -0.6305
36 D A -0.9010
37 V A 2.3287
38 I A 3.8053
39 N A 2.1674
40 F A 3.1782
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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, 1.2042 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
input 1.2042 View CSV PDB
model_9 1.1893 View CSV PDB
model_8 1.1558 View CSV PDB
model_6 0.8853 View CSV PDB
model_0 0.841 View CSV PDB
model_1 0.82 View CSV PDB
model_3 0.7176 View CSV PDB
model_10 0.6884 View CSV PDB
model_2 0.6128 View CSV PDB
model_4 0.5456 View CSV PDB
model_7 0.4227 View CSV PDB
model_5 0.2376 View CSV PDB
model_11 0.0247 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018