Project name: SP1_48 [mutate: FN29A, FD31A, IN38A, FR40A]

Status: done

Started: 2020-02-12 20:10:18
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 FN29A,FD31A,IN38A,FR40A
Energy difference between WT (input) and mutated protein (by FoldX) 2.28315 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[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                                                       (00:00:16)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:53)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:02)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:05:29)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:05:30)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:05:30)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:05:30)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:05:30)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:05:30)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:05:31)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:05:34)
[INFO]       Movie:    Creting movie with webm format                                              (00:06:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:48)
Show buried residues

Minimal score value
-1.8979
Maximal score value
1.5896
Average score
-0.4375
Total score value
-8.7507

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 0.2311
22 R A -1.8651
23 R A -1.8979
24 F A 0.1880
25 S A -0.2712
26 T A -0.7607
27 A A -0.8645
28 P A -0.8287
29 N A -1.2907 mutated: FN29A
30 A A -0.9253
31 D A -0.2277 mutated: FD31A
32 I A 1.2476
33 D A 0.5430
34 I A 1.5896
35 N A -0.5019
36 D A -1.0287
37 V A 0.8793
38 N A -0.3710 mutated: IN38A
39 N A -0.9993
40 R A -1.5966 mutated: FR40A
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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, -0.4375 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_10 -0.4375 View CSV PDB
model_5 -0.5296 View CSV PDB
model_0 -0.5824 View CSV PDB
model_8 -0.7668 View CSV PDB
model_2 -0.8451 View CSV PDB
model_3 -0.8762 View CSV PDB
model_4 -1.0069 View CSV PDB
model_11 -1.0309 View CSV PDB
input -1.0498 View CSV PDB
model_9 -1.1951 View CSV PDB
model_7 -1.2703 View CSV PDB
model_6 -1.3176 View CSV PDB
model_1 -1.4329 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018