Project name: 4D-15

Status: done

Started: 2026-04-14 03:25:35
Chain sequence(s) A: NWVNVISDLKKIEDLIQSMHIDATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEELEEKNIKEFLQSFVHIVQMFINTS
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode No
Automated mutations Yes
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]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:35)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:35)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:47)
[INFO]       AutoMutEv:Residue number 68 from chain A and a score of 2.109 omitted from automated  
                       mutation (excluded by the user).                                            (00:02:48)
[INFO]       AutoMutEv:Residue number 3 from chain A and a score of 1.544 (valine) selected for    
                       automated mutation                                                          (00:02:48)
[INFO]       AutoMutEv:Residue number 52 from chain A and a score of 1.218 (leucine) selected for  
                       automated mutation                                                          (00:02:48)
[INFO]       AutoMutEv:Residue number 45 from chain A and a score of 0.720 (leucine) selected for  
                       automated mutation                                                          (00:02:48)
[INFO]       AutoMutEv:Residue number 67 from chain A and a score of 0.700 (isoleucine) selected   
                       for automated mutation                                                      (00:02:48)
[INFO]       AutoMutEv:Residue number 80 from chain A and a score of 0.614 (valine) selected for   
                       automated mutation                                                          (00:02:48)
[INFO]       AutoMutEv:Residue number 69 from chain A and a score of 0.561 (leucine) selected for  
                       automated mutation                                                          (00:02:48)
[INFO]       AutoMutEv:Mutating residue number 3 from chain A (valine) into threonine              (00:02:48)
[INFO]       AutoMutEv:Mutating residue number 3 from chain A (valine) into alanine                (00:02:48)
[INFO]       AutoMutEv:Mutating residue number 3 from chain A (valine) into methionine             (00:02:48)
[INFO]       AutoMutEv:Mutating residue number 52 from chain A (leucine) into methionine           (00:02:52)
[INFO]       AutoMutEv:Mutating residue number 45 from chain A (leucine) into methionine           (00:02:53)
[INFO]       AutoMutEv:Mutating residue number 67 from chain A (isoleucine) into threonine         (00:02:54)
[INFO]       AutoMutEv:Mutating residue number 67 from chain A (isoleucine) into methionine        (00:03:00)
[INFO]       AutoMutEv:Mutating residue number 67 from chain A (isoleucine) into leucine           (00:03:01)
[INFO]       AutoMutEv:Mutating residue number 80 from chain A (valine) into threonine             (00:03:06)
[INFO]       AutoMutEv:Mutating residue number 80 from chain A (valine) into alanine               (00:03:09)
[INFO]       AutoMutEv:Mutating residue number 80 from chain A (valine) into methionine            (00:03:11)
[INFO]       AutoMutEv:Mutating residue number 69 from chain A (leucine) into methionine           (00:03:13)
[INFO]       AutoMutEv:Effect of mutation residue number 3 from chain A (valine) into threonine:   
                       Energy difference: -0.3560 kcal/mol, Difference in average score from the   
                       base case: -0.0189                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 3 from chain A (valine) into alanine:     
                       Energy difference: -0.0979 kcal/mol, Difference in average score from the   
                       base case: -0.0149                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 3 from chain A (valine) into methionine:  
                       Energy difference: -0.8100 kcal/mol, Difference in average score from the   
                       base case: -0.0103                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 52 from chain A (leucine) into            
                       methionine: Energy difference: 0.2987 kcal/mol, Difference in average score 
                       from the base case: -0.0065                                                 (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 45 from chain A (leucine) into            
                       methionine: Energy difference: 0.1978 kcal/mol, Difference in average score 
                       from the base case: 0.0062                                                  (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 67 from chain A (isoleucine) into         
                       threonine: Energy difference: 1.3807 kcal/mol, Difference in average score  
                       from the base case: -0.0075                                                 (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 67 from chain A (isoleucine) into         
                       methionine: Energy difference: 0.5698 kcal/mol, Difference in average score 
                       from the base case: -0.0005                                                 (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 67 from chain A (isoleucine) into         
                       leucine: Energy difference: -0.4034 kcal/mol, Difference in average score   
                       from the base case: -0.0035                                                 (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 80 from chain A (valine) into threonine:  
                       Energy difference: 0.5822 kcal/mol, Difference in average score from the    
                       base case: -0.0098                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 80 from chain A (valine) into alanine:    
                       Energy difference: 0.7253 kcal/mol, Difference in average score from the    
                       base case: -0.0094                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 80 from chain A (valine) into methionine: 
                       Energy difference: 0.0687 kcal/mol, Difference in average score from the    
                       base case: -0.0023                                                          (00:03:21)
[INFO]       AutoMutEv:Effect of mutation residue number 69 from chain A (leucine) into            
                       methionine: Energy difference: 0.6395 kcal/mol, Difference in average score 
                       from the base case: -0.0059                                                 (00:03:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:24)
Show buried residues
Minimal score value
-2.1281
Maximal score value
2.1092
Average score
-0.4486
Total score value
-51.137
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 N A -1.2730
2 W A 0.0000
3 V A 1.5439
4 N A -0.9696
5 V A 0.0000
6 I A 0.2541
7 S A -0.2618
8 D A -0.3344
9 L A 0.0000
10 K A -2.0320
11 K A -1.5526
12 I A 0.0000
13 E A -1.5313
14 D A -1.9101
15 L A 0.0395
16 I A 0.0000
17 Q A -1.2367
18 S A -0.3837
19 M A 0.0288
20 H A -0.8980
21 I A -0.2521
22 D A -1.7424
23 A A -0.3317
24 T A -0.1634
25 L A 0.0000
26 Y A 0.0702
27 T A 0.0000
28 E A -0.2359
29 S A -0.5353
30 D A -1.7804
31 V A -0.2868
32 H A -0.9938
33 P A -0.4668
34 S A -0.2393
35 C A 0.0237
36 K A -0.1805
37 V A 0.2048
38 T A 0.0231
39 A A 0.0000
40 M A 0.0000
41 K A -1.3659
42 C A 0.0000
43 F A 0.0000
44 L A 0.0000
45 L A 0.7196
46 E A 0.0000
47 L A 0.0000
48 Q A -0.4257
49 V A 0.4359
50 I A 0.0000
51 S A 0.0000
52 L A 1.2184
53 E A -1.5455
54 S A -0.4441
55 G A -0.5624
56 D A -0.5796
57 A A -0.1259
58 S A -0.1146
59 I A 0.0000
60 H A -0.9749
61 D A -1.9079
62 T A 0.0000
63 V A 0.0000
64 E A -1.5713
65 N A -1.0702
66 L A 0.0000
67 I A 0.6996
68 I A 2.1092
69 L A 0.5614
70 A A 0.0000
71 N A -0.9860
72 N A -1.4151
73 S A -0.2240
74 L A 0.1486
75 S A -0.2162
76 S A -0.4782
77 N A -1.3898
78 G A -0.9006
79 N A -1.1966
80 V A 0.6141
81 T A 0.0243
82 E A -0.3893
83 S A -0.3581
84 G A -0.4785
85 C A -0.2493
86 K A -2.0100
87 E A -2.1200
88 C A -0.5753
89 E A -2.1281
90 E A -2.1125
91 L A -0.4960
92 E A -1.9790
93 E A -1.4054
94 K A -0.7195
95 N A -0.9055
96 I A -0.2584
97 K A -1.8077
98 E A -1.1065
99 F A 0.0000
100 L A 0.0000
101 Q A -0.7899
102 S A 0.0000
103 F A 0.0000
104 V A 0.1873
105 H A -0.9242
106 I A 0.0000
107 V A 0.0000
108 Q A -0.8050
109 M A 0.0156
110 F A 0.0000
111 I A 0.3676
112 N A -1.1612
113 T A -0.3357
114 S A -0.2255
Download PDB file
View in 3Dmol

Automated mutations analysis - evolutionary conserved mutations

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated based off an evolutionary approach. The table below shows 2 best scored mutants for each mutated residue. Protein variants are ordered according to the mutation effect they had on protein stability (energetic effect) together with the difference in the average per-residue aggregation score between the wild type and the mutant (in the table green values indicate a positive change, grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this CSV file .

Mutant
Energetic effect
Score comparison
VT3A -0.356 -0.0189 View CSV PDB
VM3A -0.81 -0.0103 View CSV PDB
IL67A -0.4034 -0.0035 View CSV PDB
VM80A 0.0687 -0.0023 View CSV PDB
LM52A 0.2987 -0.0065 View CSV PDB
VT80A 0.5822 -0.0098 View CSV PDB
LM69A 0.6395 -0.0059 View CSV PDB
IT67A 1.3807 -0.0075 View CSV PDB
LM45A 0.1978 0.0062 View CSV PDB