Project name: AVIA_MU_Evolution

Status: done

Started: 2026-06-02 23:00:37
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]                                                (00:00:00)
[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 all 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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:11)
[INFO]       AutoMutEv:Residue number 28 from chain H and a score of 1.428 (phenylalanine)         
                       selected for automated mutation                                             (00:01:12)
[INFO]       AutoMutEv:Residue number 10 from chain L and a score of 1.161 (phenylalanine)         
                       selected for automated mutation                                             (00:01:12)
[INFO]       AutoMutEv:Residue number 64 from chain H and a score of 1.046 (leucine) selected for  
                       automated mutation                                                          (00:01:12)
[INFO]       AutoMutEv:Residue number 5 from chain H and a score of 0.876 (valine) selected for    
                       automated mutation                                                          (00:01:12)
[INFO]       AutoMutEv:Residue number 56 from chain L and a score of 0.824 (tryptophan) selected   
                       for automated mutation                                                      (00:01:12)
[INFO]       AutoMutEv:Residue number 114 from chain L and a score of 0.811 (tyrosine) selected    
                       for automated mutation                                                      (00:01:12)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into methionine     (00:01:12)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into tryptophan     (00:01:12)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tyrosine       (00:01:12)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into methionine     (00:01:18)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tryptophan     (00:01:19)
[INFO]       AutoMutEv:Mutating residue number 10 from chain L (phenylalanine) into tyrosine       (00:01:19)
[INFO]       AutoMutEv:Mutating residue number 64 from chain H (leucine) into methionine           (00:01:24)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into alanine                (00:01:25)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into threonine              (00:01:31)
[INFO]       AutoMutEv:Mutating residue number 56 from chain L (tryptophan) into arginine          (00:01:33)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into cysteine           (00:01:40)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into methionine             (00:01:41)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into tryptophan         (00:01:48)
[INFO]       AutoMutEv:Mutating residue number 114 from chain L (tyrosine) into histidine          (00:01:50)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       methionine: Energy difference: -0.0504 kcal/mol, Difference in average      
                       score from the base case: -0.0176                                           (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tryptophan: Energy difference: 0.4671 kcal/mol, Difference in average score 
                       from the base case: -0.0107                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tyrosine: Energy difference: -0.0487 kcal/mol, Difference in average score  
                       from the base case: -0.0072                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       methionine: Energy difference: 0.5544 kcal/mol, Difference in average score 
                       from the base case: -0.0082                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       tryptophan: Energy difference: 0.1622 kcal/mol, Difference in average score 
                       from the base case: 0.0033                                                  (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain L (phenylalanine) into      
                       tyrosine: Energy difference: 0.0040 kcal/mol, Difference in average score   
                       from the base case: 0.0024                                                  (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 64 from chain H (leucine) into            
                       methionine: Energy difference: 0.0913 kcal/mol, Difference in average score 
                       from the base case: -0.0065                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into threonine:   
                       Energy difference: 0.1734 kcal/mol, Difference in average score from the    
                       base case: -0.0386                                                          (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into alanine:     
                       Energy difference: -0.1103 kcal/mol, Difference in average score from the   
                       base case: -0.0397                                                          (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into methionine:  
                       Energy difference: -0.9149 kcal/mol, Difference in average score from the   
                       base case: -0.0143                                                          (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 56 from chain L (tryptophan) into         
                       arginine: Energy difference: -0.5928 kcal/mol, Difference in average score  
                       from the base case: -0.0408                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       histidine: Energy difference: 0.3484 kcal/mol, Difference in average score  
                       from the base case: -0.0308                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       cysteine: Energy difference: 0.4256 kcal/mol, Difference in average score   
                       from the base case: -0.0035                                                 (00:02:01)
[INFO]       AutoMutEv:Effect of mutation residue number 114 from chain L (tyrosine) into          
                       tryptophan: Energy difference: -0.5701 kcal/mol, Difference in average      
                       score from the base case: -0.0072                                           (00:02:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:07)
Show buried residues
Minimal score value
-3.1659
Maximal score value
1.4281
Average score
-0.5696
Total score value
-124.7358
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 -0.9419
2 V H -0.1059
3 Q H -0.3788
4 L H 0.0000
5 V H 0.8758
6 Q H 0.0000
7 S H -0.3281
8 G H -0.1532
9 A H 0.1521
11 E H -0.0456
12 L H 0.7684
13 K H -0.8374
14 K H -1.9473
15 P H -1.6426
16 G H -1.2135
17 A H -1.0586
18 S H -1.1563
19 V H 0.0000
20 K H -1.8841
21 L H 0.0000
22 S H -0.3712
23 C H 0.0000
24 K H -0.4592
25 A H 0.0000
26 S H -0.0172
27 G H 0.0238
28 F H 1.4281
29 T H 0.5079
30 F H 0.0000
35 T H -0.6291
36 S H -0.1381
37 Y H 0.0000
38 W H 0.4294
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 -0.9045
45 R H -1.5294
46 P H -1.1313
47 G H -1.3404
48 Q H -1.8607
49 G H -1.0796
50 L H 0.0000
51 E H -1.2795
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 0.0281
58 P H 0.0000
59 N H -1.5771
62 S H -0.6224
63 G H -0.4091
64 L H 1.0462
65 T H 0.6619
66 G H 0.2578
67 Y H -0.6385
68 N H 0.0000
69 E H -3.1659
70 K H -3.0598
71 F H -2.0646
72 K H -2.8388
74 S H -1.6789
75 K H -1.3993
76 A H 0.0000
77 T H -0.6911
78 L H 0.0000
79 T H -0.0299
80 V H -0.6511
81 D H -1.4861
82 K H -2.1831
83 S H -1.1317
84 T H -0.9627
85 S H -0.9228
86 T H 0.0000
87 A H 0.0000
88 Y H -0.2401
89 M H 0.0000
90 E H -1.1203
91 L H 0.0000
92 S H -0.8919
93 S H -0.9073
94 L H 0.0000
95 T H -1.1516
96 S H -1.3660
97 E H -1.6261
98 D H -1.1224
99 T H -0.5231
100 A H 0.0000
101 V H 0.3601
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 V H 0.0000
106 R H -0.7145
107 G H -0.9182
116 N H -1.3743
117 F H 0.0000
118 Y H -0.7257
119 G H 0.0000
120 E H -1.3580
121 G H -0.4155
122 T H -0.0893
123 L H 0.7689
124 V H 0.0000
125 T H -0.0071
126 V H 0.0000
127 S H -0.9117
128 S H -0.9179
1 D L -2.1011
2 I L -1.4654
3 Q L -1.9650
4 M L 0.0000
5 T L -0.9685
6 Q L -0.8914
7 S L -0.3077
8 P L 0.1965
9 S L 0.4267
10 F L 1.1607
11 L L 0.1725
12 S L -0.6703
13 A L 0.0000
14 S L -0.7795
15 V L 0.4571
16 G L -0.8714
17 D L -1.9944
18 R L -2.5224
19 V L -1.0757
20 T L -0.5791
21 I L 0.0000
22 T L -0.7791
23 C L 0.0000
24 K L -2.7709
25 A L 0.0000
26 S L -2.1486
27 Q L -2.7082
28 D L -2.8069
29 I L -1.3303
36 G L -1.1127
37 T L -0.3109
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 -0.8928
44 Q L -1.4504
45 K L -1.9645
46 P L -1.3159
47 G L -1.6005
48 K L -2.6940
49 A L -1.7323
50 P L 0.0000
51 K L -1.6089
52 L L -0.7384
53 L L 0.0000
54 I L 0.0000
55 Y L 0.5581
56 W L 0.8239
57 T L 0.0000
65 S L -0.2455
66 T L -0.3396
67 R L -1.0669
68 H L -0.9800
69 T L -0.5934
70 G L -0.7421
71 V L -0.5899
72 P L -0.6094
74 S L -0.7406
75 R L -1.1496
76 F L 0.0000
77 S L -0.6472
78 G L -0.3199
79 S L -0.3874
80 G L -0.8147
83 S L -0.9176
84 G L -1.7303
85 T L -2.2135
86 D L -2.1266
87 F L 0.0000
88 T L -0.6117
89 L L 0.0000
90 T L -0.6603
91 I L 0.0000
92 S L -1.6451
93 N L -1.5669
94 L L 0.0000
95 Q L -0.6273
96 S L -0.6663
97 E L -1.8143
98 D L 0.0000
99 F L -0.3792
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 0.6960
108 S L 0.0967
109 S L 0.2979
114 Y L 0.8106
115 P L -0.4650
116 L L 0.1395
117 T L -0.2951
118 F L -0.0797
119 G L 0.0000
120 A L -0.5529
121 G L 0.0000
122 T L 0.0000
123 K L -0.5843
124 L L 0.0000
125 E L -1.2588
126 I L -0.7777
127 N L -1.1971
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 -0.5928 -0.0408 View CSV PDB
VA5H -0.1103 -0.0397 View CSV PDB
VM5H -0.9149 -0.0143 View CSV PDB
FM28H -0.0504 -0.0176 View CSV PDB
YW114L -0.5701 -0.0072 View CSV PDB
FY28H -0.0487 -0.0072 View CSV PDB
YH114L 0.3484 -0.0308 View CSV PDB
LM64H 0.0913 -0.0065 View CSV PDB
FM10L 0.5544 -0.0082 View CSV PDB
FY10L 0.004 0.0024 View CSV PDB