Project name: SP1_50 [mutate: FT29A, FT31A, AL30A, IA32A, FR40A, IA38A]

Status: done

Started: 2020-02-12 21:07:09
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 IA32A,FT31A,AL30A,FT29A,IA38A,FR40A
Energy difference between WT (input) and mutated protein (by FoldX) 2.75671 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:05)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:05)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:05)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:05)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:05)
[INFO]       FoldX:    Building mutant model                                                       (00:00:27)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:04)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:20)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:05:39)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:05:39)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:05:40)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:05:46)
[INFO]       Movie:    Creting movie with webm format                                              (00:06:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:53)
Show buried residues

Minimal score value
-1.7548
Maximal score value
1.6029
Average score
0.0088
Total score value
0.1768

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 0.3634
22 R A -1.5878
23 R A -1.7548
24 F A 0.2832
25 S A -0.4383
26 T A -0.2894
27 A A 0.0836
28 P A -0.0439
29 T A 0.0435 mutated: FT29A
30 L A 0.7779 mutated: AL30A
31 T A 0.4595 mutated: FT31A
32 A A 0.2058 mutated: IA32A
33 D A 0.2087
34 I A 1.1121
35 N A -0.4811
36 D A 0.2650
37 V A 1.6029
38 A A 0.7268 mutated: IA38A
39 N A -0.1771
40 R A -1.1832 mutated: FR40A
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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, 0.0088 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_11 0.0088 View CSV PDB
model_9 -0.1124 View CSV PDB
model_8 -0.2257 View CSV PDB
model_1 -0.2345 View CSV PDB
model_4 -0.2865 View CSV PDB
model_7 -0.334 View CSV PDB
model_6 -0.4215 View CSV PDB
model_3 -0.4529 View CSV PDB
input -0.4987 View CSV PDB
model_10 -0.516 View CSV PDB
model_5 -0.6094 View CSV PDB
model_0 -0.6246 View CSV PDB
model_2 -1.0505 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018