Project name: CRH_Dynamic

Status: done

Started: 2026-06-01 19:01:36
Chain sequence(s) P: EEPPISLDLTFHLLREVLEMARAEQLAQQAHSN
input PDB
Selected Chain(s) P
Distance of aggregation 5 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]                                                (00:00:00)
[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 P chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:26)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:02:58)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:02:59)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:02:59)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:02:59)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:00)
Show buried residues
Minimal score value
-2.2448
Maximal score value
2.1031
Average score
-0.129
Total score value
-4.2554
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
2 E P -2.1687
3 E P -2.2448
4 P P -0.6587
5 P P -0.1130
6 I P 1.7459
7 S P 0.5231
8 L P 1.1897
9 D P -1.0251
10 L P 1.0548
11 T P 0.5795
12 F P 1.8038
13 H P -0.1200
14 L P 1.6023
15 L P 1.8305
16 R P -1.0302
17 E P -0.8012
18 V P 2.1031
19 L P 1.7339
20 E P -0.5803
21 M P 0.9289
22 A P 0.0308
23 R P -1.9168
24 A P -0.4439
25 E P -1.8927
26 Q P -1.3430
27 L P 1.3352
28 A P -0.0857
29 Q P -1.5364
30 Q P -1.4117
31 A P -0.3672
32 H P -1.0194
33 S P -0.6446
34 N P -1.3135
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, -0.129 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_4 -0.129 View CSV PDB
model_8 -0.202 View CSV PDB
model_11 -0.216 View CSV PDB
model_0 -0.2178 View CSV PDB
model_10 -0.2248 View CSV PDB
CABS_average -0.2525 View CSV PDB
model_2 -0.2669 View CSV PDB
model_5 -0.2778 View CSV PDB
model_6 -0.2838 View CSV PDB
model_9 -0.2906 View CSV PDB
model_3 -0.2983 View CSV PDB
model_1 -0.3072 View CSV PDB
model_7 -0.316 View CSV PDB
input -0.3594 View CSV PDB