Project name: AVIA_HU_Evolution

Status: done

Started: 2026-06-02 22:58:40
Chain sequence(s) H: QVQLVQSGAELKKPGASVKLSCKASGFTFTSYWMHWVRQRPGQGLEWIGMIHPNSGLTGYNEKFKSKATLTVDKSTSTAYMELSSLTSEDTAVYYCVRGNFYGEGTLVTVSS
L: DIQMTQSPSFLSASVGDRVTITCKASQDIGTAVAWYQQKPGKAPKLLIYWTSTRHTGVPSRFSGSGSGTDFTLTISNLQSEDFATYFCQQYSSYPLTFGAGTKLEIN
input PDB
Selected Chain(s) H,L
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
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 all 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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:08)
[INFO]       AutoMutEv:Residue number 28 from chain H and a score of 1.436 (phenylalanine)         
                       selected for automated mutation                                             (00:01:09)
[INFO]       AutoMutEv:Residue number 10 from chain L and a score of 1.132 (phenylalanine)         
                       selected for automated mutation                                             (00:01:09)
[INFO]       AutoMutEv:Residue number 64 from chain H and a score of 1.047 (leucine) selected for  
                       automated mutation                                                          (00:01:09)
[INFO]       AutoMutEv:Residue number 56 from chain L and a score of 0.803 (tryptophan) selected   
                       for automated mutation                                                      (00:01:09)
[INFO]       AutoMutEv:Residue number 12 from chain H and a score of 0.758 (leucine) selected for  
                       automated mutation                                                          (00:01:09)
[INFO]       AutoMutEv:Residue number 114 from chain L and a score of 0.751 (tyrosine) selected    
                       for automated mutation                                                      (00:01:09)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into methionine     (00:01:09)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tryptophan     (00:01:09)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tyrosine       (00:01:09)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into methionine     (00:01:15)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into tryptophan     (00:01:15)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into tyrosine       (00:01:17)
[INFO]       AutoMutEv:Mutating residue number 64 from chain H (leucine) into methionine           (00:01:23)
[INFO]       AutoMutEv:Mutating residue number 56 from chain L (tryptophan) into arginine          (00:01:26)
[INFO]       AutoMutEv:Mutating residue number 12 from chain H (leucine) into methionine           (00:01:28)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into histidine          (00:01:34)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into cysteine           (00:01:35)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into tryptophan         (00:01:42)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       methionine: Energy difference: 0.0268 kcal/mol, Difference in average score 
                       from the base case: -0.0158                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tryptophan: Energy difference: 0.3907 kcal/mol, Difference in average score 
                       from the base case: -0.0096                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tyrosine: Energy difference: -0.0432 kcal/mol, Difference in average score  
                       from the base case: -0.0078                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       methionine: Energy difference: 0.8395 kcal/mol, Difference in average score 
                       from the base case: -0.0072                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       tryptophan: Energy difference: 0.2311 kcal/mol, Difference in average score 
                       from the base case: 0.0041                                                  (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       tyrosine: Energy difference: 0.0174 kcal/mol, Difference in average score   
                       from the base case: 0.0024                                                  (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 64 from chain H (leucine) into            
                       methionine: Energy difference: 0.1002 kcal/mol, Difference in average score 
                       from the base case: -0.0080                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 56 from chain L (tryptophan) into         
                       arginine: Energy difference: -0.5180 kcal/mol, Difference in average score  
                       from the base case: -0.0417                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 12 from chain H (leucine) into            
                       methionine: Energy difference: -0.0710 kcal/mol, Difference in average      
                       score from the base case: -0.0072                                           (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       histidine: Energy difference: 0.3274 kcal/mol, Difference in average score  
                       from the base case: -0.0244                                                 (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       cysteine: Energy difference: 0.4489 kcal/mol, Difference in average score   
                       from the base case: 0.0007                                                  (00:01:49)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       tryptophan: Energy difference: -0.1505 kcal/mol, Difference in average      
                       score from the base case: -0.0049                                           (00:01:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:54)
Show buried residues
Minimal score value
-3.1814
Maximal score value
1.4357
Average score
-0.5714
Total score value
-125.1428
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 Q H -0.9383
2 V H -0.0984
3 Q H -0.4665
4 L H 0.0000
5 V H 0.6514
6 Q H 0.0000
7 S H -0.4263
8 G H -0.1572
9 A H 0.1370
11 E H -0.0603
12 L H 0.7585
13 K H -0.8497
14 K H -1.9505
15 P H -1.6392
16 G H -1.2148
17 A H -1.0486
18 S H -1.1423
19 V H 0.0000
20 K H -1.8744
21 L H 0.0000
22 S H -0.4459
23 C H 0.0000
24 K H -0.7882
25 A H 0.0000
26 S H -0.1070
27 G H 0.0153
28 F H 1.4357
29 T H 0.5073
30 F H 0.0000
35 T H -0.6064
36 S H -0.0350
37 Y H 0.1234
38 W H 0.5354
39 M H 0.0000
40 H H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -0.8076
45 R H -1.4776
46 P H -1.1472
47 G H -1.3456
48 Q H -1.8033
49 G H -0.9705
50 L H 0.0000
51 E H -0.8137
52 W H 0.0000
53 I H 0.0000
54 G H 0.0000
55 M H 0.0000
56 I H 0.0000
57 H H 0.0806
58 P H 0.0000
59 N H -1.5203
62 S H -0.6410
63 G H -0.4193
64 L H 1.0471
65 T H 0.6500
66 G H 0.1174
67 Y H -0.7126
68 N H 0.0000
69 E H -3.1814
70 K H -3.0091
71 F H -2.0594
72 K H -2.8339
74 S H -1.6506
75 K H -1.3258
76 A H 0.0000
77 T H -0.6460
78 L H 0.0000
79 T H -0.0313
80 V H -0.7267
81 D H -1.4445
82 K H -2.2717
83 S H -1.1800
84 T H -1.0530
85 S H -1.0727
86 T H -0.8136
87 A H 0.0000
88 Y H -0.2672
89 M H 0.0000
90 E H -1.0724
91 L H 0.0000
92 S H -0.8634
93 S H -0.8994
94 L H 0.0000
95 T H -1.1280
96 S H -1.3233
97 E H -1.5335
98 D H -1.1047
99 T H -0.5176
100 A H 0.0000
101 V H 0.3107
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 V H 0.0000
106 R H -0.6237
107 G H -0.9049
116 N H -1.4531
117 F H 0.0000
118 Y H -0.8181
119 G H 0.0000
120 E H -1.7773
121 G H -0.6278
122 T H -0.1853
123 L H 0.7390
124 V H 0.0000
125 T H -0.0139
126 V H 0.0000
127 S H -0.9042
128 S H -0.9196
1 D L -2.1255
2 I L -1.4909
3 Q L -1.9689
4 M L 0.0000
5 T L -0.9182
6 Q L 0.0000
7 S L -0.2767
8 P L 0.2315
9 S L 0.4512
10 F L 1.1324
11 L L 0.1242
12 S L -0.7316
13 A L 0.0000
14 S L -0.7979
15 V L 0.4535
16 G L -0.8280
17 D L -1.9639
18 R L -2.5079
19 V L -1.0643
20 T L -0.6151
21 I L 0.0000
22 T L -0.7632
23 C L 0.0000
24 K L -2.7564
25 A L 0.0000
26 S L -2.1512
27 Q L -2.7100
28 D L -2.8138
29 I L -1.3558
36 G L -1.1151
37 T L -0.3181
38 A L 0.0000
39 V L 0.0000
40 A L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.7799
44 Q L -1.2460
45 K L -1.6265
46 P L -1.1325
47 G L -1.4566
48 K L -2.5390
49 A L -1.7499
50 P L 0.0000
51 K L -1.5334
52 L L -0.7260
53 L L 0.0000
54 I L 0.0000
55 Y L 0.5436
56 W L 0.8031
57 T L 0.0000
65 S L -0.2582
66 T L -0.3610
67 R L -1.0974
68 H L -1.0063
69 T L -0.6033
70 G L -0.7412
71 V L -0.5954
72 P L -0.6348
74 S L -0.7684
75 R L -1.1890
76 F L 0.0000
77 S L -0.6678
78 G L -0.3166
79 S L -0.3698
80 G L -0.8013
83 S L -0.9100
84 G L -1.7326
85 T L -2.2225
86 D L -2.1452
87 F L 0.0000
88 T L -0.6211
89 L L 0.0000
90 T L -0.6675
91 I L 0.0000
92 S L -1.6689
93 N L -1.5239
94 L L 0.0000
95 Q L -0.6830
96 S L -0.7260
97 E L -1.7982
98 D L 0.0000
99 F L -0.3955
100 A L 0.0000
101 T L 0.0000
102 Y L 0.0000
103 F L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 Q L 0.0000
107 Y L 0.6491
108 S L 0.0749
109 S L 0.2629
114 Y L 0.7510
115 P L -0.5154
116 L L 0.0000
117 T L -0.2823
118 F L 0.0010
119 G L 0.0000
120 A L -0.4681
121 G L 0.0000
122 T L 0.0000
123 K L -0.5888
124 L L 0.0000
125 E L -1.4386
126 I L -0.8815
127 N L -1.2433
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
WR56L -0.518 -0.0417 View CSV PDB
FY28H -0.0432 -0.0078 View CSV PDB
LM12H -0.071 -0.0072 View CSV PDB
YW114L -0.1505 -0.0049 View CSV PDB
FM28H 0.0268 -0.0158 View CSV PDB
LM64H 0.1002 -0.008 View CSV PDB
YH114L 0.3274 -0.0244 View CSV PDB
FM10L 0.8395 -0.0072 View CSV PDB
FY10L 0.0174 0.0024 View CSV PDB