Project name: 00254

Status: done

Started: 2025-08-01 20:40:36
Chain sequence(s) H: QVQLVESGGVLVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSYIRSGHGNTFYADSVKGRFTISRDNAKNSLYLQLNSLRAEDTAVYYCARGERTGDYTGGMDVWGQGTTVTVSS
L: DIQMTQSPSSLSASVGDRVTITCRASQGIHHDLGWYQQKPGKAPKRLIYHASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPFTFGPGTKVDIK
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                                          (00:01:27)
[INFO]       AutoMutEv:Residue number 11 from chain H and a score of 2.120 (valine) selected for   
                       automated mutation                                                          (00:01:28)
[INFO]       AutoMutEv:Residue number 12 from chain H and a score of 1.998 (leucine) selected for  
                       automated mutation                                                          (00:01:28)
[INFO]       AutoMutEv:Residue number 28 from chain H and a score of 1.246 (phenylalanine)         
                       selected for automated mutation                                             (00:01:28)
[INFO]       AutoMutEv:Residue number 5 from chain H and a score of 0.715 (valine) selected for    
                       automated mutation                                                          (00:01:28)
[INFO]       AutoMutEv:Residue number 9 from chain H and a score of 0.448 (glycine) selected for   
                       automated mutation                                                          (00:01:28)
[INFO]       AutoMutEv:Residue number 29 from chain H and a score of 0.344 (threonine) selected    
                       for automated mutation                                                      (00:01:28)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into threonine             (00:01:28)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into methionine            (00:01:28)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into methionine     (00:01:28)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into alanine               (00:01:34)
[INFO]       AutoMutEv:Mutating residue number 12 from chain H (leucine) into methionine           (00:01:36)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tryptophan     (00:01:37)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tyrosine       (00:01:40)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into alanine                (00:01:43)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into glutamic acid         (00:01:43)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into threonine              (00:01:46)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into methionine             (00:01:49)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into aspartic acid         (00:01:50)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into asparagine            (00:01:51)
[INFO]       AutoMutEv:Mutating residue number 29 from chain H (threonine) into aspartic acid      (00:01:56)
[INFO]       AutoMutEv:Mutating residue number 29 from chain H (threonine) into glutamic acid      (00:01:57)
[INFO]       AutoMutEv:Mutating residue number 29 from chain H (threonine) into lysine             (00:02:02)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into threonine:  
                       Energy difference: 0.1622 kcal/mol, Difference in average score from the    
                       base case: -0.0266                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into alanine:    
                       Energy difference: 0.1521 kcal/mol, Difference in average score from the    
                       base case: -0.0243                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into methionine: 
                       Energy difference: -0.6189 kcal/mol, Difference in average score from the   
                       base case: -0.0105                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 12 from chain H (leucine) into            
                       methionine: Energy difference: 0.0919 kcal/mol, Difference in average score 
                       from the base case: -0.0072                                                 (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       methionine: Energy difference: -0.7008 kcal/mol, Difference in average      
                       score from the base case: -0.0196                                           (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tryptophan: Energy difference: -0.1364 kcal/mol, Difference in average      
                       score from the base case: -0.0166                                           (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tyrosine: Energy difference: 0.2998 kcal/mol, Difference in average score   
                       from the base case: -0.0094                                                 (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into threonine:   
                       Energy difference: 0.1087 kcal/mol, Difference in average score from the    
                       base case: -0.0183                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into alanine:     
                       Energy difference: -0.2053 kcal/mol, Difference in average score from the   
                       base case: -0.0186                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into methionine:  
                       Energy difference: -0.5338 kcal/mol, Difference in average score from the   
                       base case: -0.0056                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into glutamic    
                       acid: Energy difference: 4.4554 kcal/mol, Difference in average score from  
                       the base case: -0.0133                                                      (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into aspartic    
                       acid: Energy difference: 3.1828 kcal/mol, Difference in average score from  
                       the base case: -0.0143                                                      (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into asparagine: 
                       Energy difference: 1.8612 kcal/mol, Difference in average score from the    
                       base case: -0.0108                                                          (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 29 from chain H (threonine) into glutamic 
                       acid: Energy difference: 0.4193 kcal/mol, Difference in average score from  
                       the base case: -0.0238                                                      (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 29 from chain H (threonine) into aspartic 
                       acid: Energy difference: 0.9978 kcal/mol, Difference in average score from  
                       the base case: -0.0291                                                      (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 29 from chain H (threonine) into lysine:  
                       Energy difference: -0.2218 kcal/mol, Difference in average score from the   
                       base case: -0.0213                                                          (00:02:18)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:24)
Show buried residues
Minimal score value
-2.8941
Maximal score value
2.1205
Average score
-0.5722
Total score value
-131.0274
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 -0.9177
2 V H 0.0994
3 Q H -0.2122
4 L H 0.0000
5 V H 0.7154
6 E H 0.0000
7 S H -0.2802
8 G H -0.3005
9 G H 0.4479
11 V H 2.1205
12 L H 1.9975
13 V H 0.1719
14 K H -1.8931
15 P H -2.0704
16 G H -1.6258
17 G H -1.3314
18 S H -1.1510
19 L H -0.7547
20 R H -1.7962
21 L H 0.0000
22 S H -0.4414
23 C H 0.0000
24 A H -0.0902
25 A H 0.0813
26 S H 0.0561
27 G H -0.0213
28 F H 1.2465
29 T H 0.3442
30 F H 0.0000
35 S H -1.0529
36 D H -1.3606
37 Y H 0.0000
38 Y H 0.0000
39 M H 0.0000
40 S H 0.0000
41 W H 0.0000
42 I H 0.0000
43 R H 0.0000
44 Q H -0.4784
45 A H 0.0000
46 P H -0.7498
47 G H -1.0244
48 K H -1.1818
49 G H -0.6759
50 L H 0.0000
51 E H -0.2793
52 W H 0.0722
53 V H 0.0000
54 S H 0.0000
55 Y H 0.3374
56 I H 0.0000
57 R H -1.1946
58 S H 0.0000
59 G H -1.6058
62 H H -1.6902
63 G H -1.3144
64 N H -0.9511
65 T H -0.3106
66 F H 0.3139
67 Y H -0.4861
68 A H -1.1687
69 D H -2.4472
70 S H -1.7432
71 V H 0.0000
72 K H -2.4847
74 G H -1.7737
75 R H -1.6745
76 F H 0.0000
77 T H -0.6494
78 I H 0.0000
79 S H -0.4266
80 R H -1.1592
81 D H -1.6732
82 N H -1.8622
83 A H -1.3926
84 K H -2.2414
85 N H -1.4674
86 S H 0.0000
87 L H 0.0000
88 Y H -0.3581
89 L H 0.0000
90 Q H -1.0176
91 L H 0.0000
92 N H -1.2937
93 S H -1.4070
94 L H 0.0000
95 R H -2.8941
96 A H -2.0254
97 E H -2.4160
98 D H 0.0000
99 T H -0.7429
100 A H 0.0000
101 V H -0.3017
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H -0.3720
107 G H 0.0000
108 E H -1.4203
109 R H -2.1248
110 T H -1.4997
111 G H -1.6918
111A D H -2.2395
112A Y H -1.2158
112 T H -1.0500
113 G H 0.0000
114 G H 0.0000
115 M H 0.0000
116 D H -0.3708
117 V H 0.0102
118 W H -0.1473
119 G H 0.0000
120 Q H -1.2584
121 G H -0.8310
122 T H 0.0000
123 T H 0.2915
124 V H 0.0000
125 T H 0.2465
126 V H 0.0000
127 S H -0.8346
128 S H -0.7891
1 D L -2.1514
2 I L 0.0000
3 Q L -1.8898
4 M L 0.0000
5 T L -0.6649
6 Q L 0.0000
7 S L -0.4458
8 P L -0.5686
9 S L -0.6879
10 S L -0.7241
11 L L -0.4091
12 S L -0.7419
13 A L 0.0000
14 S L -0.6702
15 V L 0.2105
16 G L -0.6352
17 D L -1.3250
18 R L -2.2039
19 V L 0.0000
20 T L -0.5926
21 I L 0.0000
22 T L -0.5519
23 C L 0.0000
24 R L -1.7493
25 A L 0.0000
26 S L -1.5758
27 Q L -1.8004
28 G L -1.4938
29 I L 0.0000
36 H L -2.0717
37 H L -1.9985
38 D L -1.4469
39 L L 0.0000
40 G L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.5232
44 Q L 0.0000
45 K L -1.3523
46 P L -1.0998
47 G L -1.6149
48 K L -2.3398
49 A L -1.2827
50 P L 0.0000
51 K L -0.6522
52 R L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.2000
56 H L -1.1812
57 A L 0.0000
65 S L -0.5759
66 S L -0.1927
67 L L 0.1832
68 Q L -0.1337
69 S L -0.3925
70 G L -0.4888
71 V L -0.2808
72 P L -0.4552
74 S L -0.5831
75 R L -1.0730
76 F L 0.0000
77 S L -0.3957
78 G L -0.2775
79 S L -0.6131
80 G L -1.2106
83 S L -1.3657
84 G L -1.4593
85 T L -1.5865
86 E L -1.8924
87 F L 0.0000
88 T L -0.5498
89 L L 0.0000
90 T L -0.6088
91 I L 0.0000
92 S L -1.3233
93 S L -1.0355
94 L L 0.0000
95 Q L -0.6725
96 P L -0.6682
97 E L -1.7319
98 D L 0.0000
99 F L 0.0590
100 A L 0.0000
101 T L -0.4669
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 L L 0.0000
106 Q L 0.0000
107 H L 0.0000
108 N L -1.3977
109 S L -0.4748
114 Y L 0.1316
115 P L -0.5852
116 F L 0.0000
117 T L -0.2984
118 F L 0.2843
119 G L 0.0000
120 P L -0.3272
121 G L 0.0000
122 T L 0.0000
123 K L -0.9094
124 V L 0.0000
125 D L -0.3324
126 I L -0.3143
127 K L -1.4232
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
FM28H -0.7008 -0.0196 View CSV PDB
TK29H -0.2218 -0.0213 View CSV PDB
VA5H -0.2053 -0.0186 View CSV PDB
VM11H -0.6189 -0.0105 View CSV PDB
FW28H -0.1364 -0.0166 View CSV PDB
VM5H -0.5338 -0.0056 View CSV PDB
VT11H 0.1622 -0.0266 View CSV PDB
LM12H 0.0919 -0.0072 View CSV PDB
TE29H 0.4193 -0.0238 View CSV PDB
GN9H 1.8612 -0.0108 View CSV PDB
GD9H 3.1828 -0.0143 View CSV PDB