Project name: SP1_49 [mutate: FT29A, FT31A, IA32A, IA38A, FR40A]

Status: done

Started: 2020-02-12 20:44:11
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,IA38A,FR40A,IA32A
Energy difference between WT (input) and mutated protein (by FoldX) 3.43527 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:04)
[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                                                       (00:00:22)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:07)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:23)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:05:42)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:05:43)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:05:44)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:05:44)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:05:44)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:05:44)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:05:47)
[INFO]       Movie:    Creting movie with webm format                                              (00:06:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:52)
Show buried residues

Minimal score value
-2.0936
Maximal score value
1.4265
Average score
-0.237
Total score value
-4.7394

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 0.4153
22 R A -1.7218
23 R A -1.7623
24 F A 0.2017
25 S A -0.4347
26 T A 0.2010
27 A A -0.0636
28 P A -0.3657
29 T A -0.3175 mutated: FT29A
30 A A -0.7492
31 T A -0.2509 mutated: FT31A
32 A A -0.0027 mutated: IA32A
33 D A -0.1940
34 I A 1.3580
35 N A -0.1348
36 D A 0.2198
37 V A 1.4265
38 A A 0.3437 mutated: IA38A
39 N A -0.8146
40 R A -2.0936 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, -0.237 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_5 -0.237 View CSV PDB
model_0 -0.3079 View CSV PDB
model_6 -0.3974 View CSV PDB
input -0.5256 View CSV PDB
model_9 -0.5458 View CSV PDB
model_11 -0.5462 View CSV PDB
model_10 -0.6591 View CSV PDB
model_4 -0.6923 View CSV PDB
model_1 -0.6952 View CSV PDB
model_2 -0.6957 View CSV PDB
model_3 -0.7182 View CSV PDB
model_7 -1.3168 View CSV PDB
model_8 -1.4553 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018