Project name: open_traj_prpcs_dynamic

Status: done

Started: 2026-03-17 18:38:32
Chain sequence(s) A: LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQR
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:24)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:13:31)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:13:31)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:13:31)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:13:31)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:13:32)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:13:32)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:13:32)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:13:33)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:13:33)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:13:33)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:13:34)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:13:34)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:13:34)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:13:36)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:37)
Show buried residues
Minimal score value
-2.9595
Maximal score value
1.7127
Average score
-0.7131
Total score value
-74.1626
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 L A 1.3385
2 G A 0.9390
3 G A 0.9100
4 Y A 1.5309
5 M A 1.4740
6 L A 1.7127
7 G A 0.6138
8 S A 0.0956
9 A A -0.2914
10 M A -0.3519
11 S A -0.9154
12 R A -1.3103
13 P A -0.5156
14 I A 0.0000
15 I A 0.7038
16 H A 0.5105
17 F A 1.2491
18 G A 0.0565
19 S A -0.5020
20 D A -1.5388
21 Y A -0.1892
22 E A -0.9806
23 D A 0.0000
24 R A -2.4491
25 Y A -1.6047
26 Y A 0.0000
27 R A -2.6676
28 E A -2.8198
29 N A 0.0000
30 M A -1.3806
31 H A -1.2349
32 R A -1.0488
33 Y A 0.0000
34 P A 0.0000
35 N A -0.9131
36 Q A 0.0000
37 V A 0.0000
38 Y A 0.0000
39 Y A -0.0712
40 R A -1.0604
41 P A -0.8805
42 M A -0.8920
43 D A -2.0805
44 E A -2.0426
45 Y A -1.3103
46 S A -1.0677
47 N A -1.3908
48 Q A 0.0000
49 N A -2.0764
50 N A -2.4106
51 F A 0.0000
52 V A 0.0000
53 H A -2.6787
54 D A -2.7807
55 C A 0.0000
56 V A 0.0000
57 N A -1.8431
58 I A -0.7609
59 T A 0.0000
60 I A 0.0000
61 K A -1.1502
62 Q A -0.1695
63 H A 0.0000
64 T A 0.4925
65 V A 1.3593
66 T A 0.1439
67 T A 0.0000
68 T A -0.0539
69 T A -0.8752
70 K A -2.2823
71 G A -1.9145
72 E A -2.3113
73 N A -1.1390
74 F A 0.5453
75 T A -1.0574
76 E A -1.8381
77 T A -1.3711
78 D A 0.0000
79 V A -1.4646
80 K A -2.6637
81 M A 0.0000
82 M A 0.0000
83 E A -2.5825
84 R A -1.9802
85 V A 0.0000
86 V A 0.0000
87 E A -1.2523
88 Q A -0.6326
89 M A 0.0000
90 C A 0.0000
91 I A -0.5044
92 T A -0.9732
93 Q A -1.2382
94 Y A 0.0000
95 E A -2.7319
96 R A -2.9595
97 E A -1.9171
98 S A -1.9677
99 Q A 0.0000
100 A A -0.6171
101 Y A -0.7017
102 Y A -1.3281
103 Q A -2.0153
104 R A -2.0852
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, -0.7131 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_8 -0.7131 View CSV PDB
model_3 -0.7924 View CSV PDB
model_1 -0.8029 View CSV PDB
model_10 -0.8052 View CSV PDB
model_0 -0.8352 View CSV PDB
model_4 -0.8623 View CSV PDB
model_6 -0.8634 View CSV PDB
model_9 -0.8643 View CSV PDB
CABS_average -0.867 View CSV PDB
model_2 -0.896 View CSV PDB
model_5 -0.9273 View CSV PDB
input -0.9468 View CSV PDB
model_7 -1.0159 View CSV PDB
model_11 -1.0262 View CSV PDB