Project name: c1 prime from self pdb

Status: done

Started: 2026-03-09 15:34:04
Chain sequence(s) A: EVQLVESGGGLVQPGGSLRLSCAASGRTFSSYAMSWFRQAPGKEREFVSAISRSAGTTRYADSVKGRFTISRDNSKNTLYLQMNSLRPEDTAVYYCAAATLQSTVVLSTHNYDYWGQGTLVTVSS
input PDB
Selected Chain(s) A
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:29)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:21:10)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:21:11)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:21:11)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:21:12)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:21:12)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:21:12)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:21:13)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:21:13)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:21:14)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:21:14)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:21:15)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:21:15)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:21:16)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:21:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:19)
Show buried residues
Minimal score value
-2.386
Maximal score value
1.7728
Average score
-0.2499
Total score value
-31.2393
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 E A -1.8199
2 V A 0.0000
3 Q A -1.1983
4 L A 0.0000
5 V A 1.5537
6 E A -0.0989
7 S A -0.3145
8 G A -0.2719
9 G A -0.5203
10 G A 0.0655
11 L A 1.5215
12 V A 0.0000
13 Q A -0.9243
14 P A -0.4484
15 G A -0.5796
16 G A -0.6087
17 S A -0.2808
18 L A 0.0000
19 R A -1.8441
20 L A 0.0000
21 S A 0.0250
22 C A 0.0000
23 A A 0.0118
24 A A 0.0000
25 S A -0.1811
26 G A -0.8378
27 R A -1.9472
28 T A -0.4256
29 F A 0.0000
30 S A -0.1474
31 S A -0.0826
32 Y A 0.0000
33 A A 0.0000
34 M A 0.0000
35 S A 0.0000
36 W A 0.0000
37 F A 0.0000
38 R A 0.0000
39 Q A -0.5890
40 A A -0.1178
41 P A -0.3424
42 G A -0.7331
43 K A -1.5773
44 E A -2.3860
45 R A -2.2321
46 E A 0.0000
47 F A 0.6883
48 V A 0.0000
49 S A 0.0000
50 A A 0.0000
51 I A 0.0000
52 S A 0.0000
53 R A -0.7409
54 S A -0.3399
55 A A -0.1884
56 G A -0.4729
57 T A -0.1538
58 T A -0.3175
59 R A -1.2127
60 Y A -0.0424
61 A A 0.0000
62 D A -1.8288
63 S A -0.5445
64 V A 0.0000
65 K A -1.7182
66 G A -0.7782
67 R A -1.6802
68 F A 0.0000
69 T A -0.0305
70 I A 0.0000
71 S A -0.1262
72 R A -0.4356
73 D A -0.8032
74 N A -0.4453
75 S A -0.5852
76 K A -1.8009
77 N A -0.6685
78 T A -0.0683
79 L A 0.0000
80 Y A 0.7397
81 L A 0.0000
82 Q A -0.4790
83 M A 0.0000
84 N A -1.1525
85 S A -0.2047
86 L A 0.7105
87 R A 0.0000
88 P A -0.5570
89 E A -1.8560
90 D A 0.0000
91 T A -0.0448
92 A A 0.0000
93 V A 0.5798
94 Y A 0.0000
95 Y A -0.0275
96 C A 0.0000
97 A A 0.0000
98 A A 0.0000
99 A A 0.0000
100 T A 0.2369
101 L A 1.4882
102 Q A -0.0215
103 S A -0.2753
104 T A -0.1423
105 V A 0.0000
106 V A 1.7728
107 L A 0.0000
108 S A -0.0741
109 T A -0.1082
110 H A -0.6180
111 N A -1.0998
112 Y A 1.0388
113 D A 0.0743
114 Y A 0.4361
115 W A 1.2262
116 G A -0.0478
117 Q A -1.2747
118 G A -0.6760
119 T A 0.0000
120 L A 1.0601
121 V A 0.0000
122 T A 0.0199
123 V A 0.1332
124 S A -0.2380
125 S A -0.2332
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, -0.2499 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 -0.2499 View CSV PDB
model_4 -0.2527 View CSV PDB
model_2 -0.2591 View CSV PDB
model_3 -0.26 View CSV PDB
CABS_average -0.2911 View CSV PDB
model_6 -0.296 View CSV PDB
model_8 -0.2964 View CSV PDB
model_0 -0.2995 View CSV PDB
model_9 -0.2998 View CSV PDB
model_7 -0.3104 View CSV PDB
model_5 -0.312 View CSV PDB
model_1 -0.3133 View CSV PDB
input -0.3184 View CSV PDB
model_10 -0.344 View CSV PDB