Project name: KM005_lineal_cap_cluster0_Aggrescan4D_2

Status: done

Started: 2024-04-29 16:21:46
Chain sequence(s) A: RYRPGTVALREIRRYQKSTE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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             (00:00:05)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:05)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:05)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:23)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:02:27)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:28)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:32)
Show buried residues
Minimal score value
-2.6609
Maximal score value
1.4538
Average score
-0.8069
Total score value
-16.1376
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 R A -1.6850
2 Y A -0.5555
3 R A -2.1520
4 P A -1.7632
5 G A -0.7374
6 T A 0.2349
7 V A 1.4538
8 A A 0.8422
9 L A 0.5658
10 R A -0.3912
11 E A 0.3422
12 I A 1.2026
13 R A -1.0902
14 R A -1.6457
15 Y A -0.2547
16 Q A -1.5932
17 K A -2.3240
18 S A -1.8697
19 T A -2.0564
20 E A -2.6609
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D 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 A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.8069 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 A4D Score
model_11 -0.8069 View CSV PDB
model_9 -1.1097 View CSV PDB
model_0 -1.2567 View CSV PDB
input -1.291 View CSV PDB
model_5 -1.2916 View CSV PDB
model_4 -1.3046 View CSV PDB
model_7 -1.3931 View CSV PDB
model_8 -1.4548 View CSV PDB
CABS_average -1.4598 View CSV PDB
model_2 -1.4944 View CSV PDB
model_3 -1.5983 View CSV PDB
model_6 -1.8885 View CSV PDB
model_10 -1.9214 View CSV PDB
model_1 -1.9978 View CSV PDB