Project name: 2043

Status: done

Started: 2020-02-10 13:33:03
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
Downloads Download all the data
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             (00:00:06)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:06)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:06)
[CRITICAL]   FoldX:    FoldX encountered an error: FoldX didn't produce expected repair files.     
                       Can't continue without it. This is unexpected and could indicate FoldX      
                       issues.                                                                     (00:00:16)
[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]       CABS:     Running CABS flex simulation                                                (00:00:15)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:04:34)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:04:35)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:04:35)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:36)
[INFO]       Movie:    Creting movie with webm format                                              (00:05:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:39)
Show buried residues

Minimal score value
-1.5149
Maximal score value
3.8846
Average score
1.4342
Total score value
28.6843

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 1.3113
22 R A -1.5149
23 R A -0.9525
24 F A 1.1455
25 S A 0.7274
26 T A 1.1816
27 A A 1.2208
28 P A 1.2132
29 F A 2.9164
30 A A 2.4784
31 F A 3.0042
32 I A 3.1206
33 D A 0.4927
34 I A 1.5987
35 N A -0.5931
36 D A -0.8398
37 V A 2.4363
38 I A 3.8846
39 N A 2.3456
40 F A 3.5073
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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, 1.4342 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 1.4342 View CSV PDB
model_9 1.2499 View CSV PDB
model_1 1.0384 View CSV PDB
model_6 1.0056 View CSV PDB
model_10 0.931 View CSV PDB
model_2 0.8858 View CSV PDB
model_3 0.8196 View CSV PDB
model_0 0.7936 View CSV PDB
model_8 0.7646 View CSV PDB
model_11 0.7624 View CSV PDB
model_5 0.7458 View CSV PDB
model_7 0.6019 View CSV PDB
model_4 0.5443 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018