Project name: 00257

Status: done

Started: 2025-08-01 20:44:03
Chain sequence(s) H: QVQLVESGGVLVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSYIRSGHGNTFYADSVKGRFTISRDNAKNSLYLQLNSLRAEDTAVYYCARGERHGHYEGGMDVWGQGTTVTVSS
L: DIQMTQSPSSLSASVGDRVTITCRASQGIHHDLGWYQQKPGKAPKRLIYAASRLDSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCLQHNSYPFTFGPGTKVDIK
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                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:43)
[INFO]       AutoMutEv:Residue number 11 from chain H and a score of 2.165 (valine) selected for   
                       automated mutation                                                          (00:01:45)
[INFO]       AutoMutEv:Residue number 12 from chain H and a score of 1.994 (leucine) selected for  
                       automated mutation                                                          (00:01:45)
[INFO]       AutoMutEv:Residue number 28 from chain H and a score of 1.064 (phenylalanine)         
                       selected for automated mutation                                             (00:01:45)
[INFO]       AutoMutEv:Residue number 15 from chain L and a score of 0.684 (valine) selected for   
                       automated mutation                                                          (00:01:45)
[INFO]       AutoMutEv:Residue number 9 from chain H and a score of 0.511 (glycine) selected for   
                       automated mutation                                                          (00:01:45)
[INFO]       AutoMutEv:Residue number 5 from chain H and a score of 0.505 (valine) selected for    
                       automated mutation                                                          (00:01:45)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into methionine            (00:01:45)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into methionine     (00:01:45)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into threonine             (00:01:45)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into alanine               (00:01:51)
[INFO]       AutoMutEv:Mutating residue number 12 from chain H (leucine) into methionine           (00:01:53)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tryptophan     (00:01:54)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tyrosine       (00:01:57)
[INFO]       AutoMutEv:Mutating residue number 15 from chain L (valine) into alanine               (00:02:00)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into glutamic acid         (00:02:03)
[INFO]       AutoMutEv:Mutating residue number 15 from chain L (valine) into threonine             (00:02:03)
[INFO]       AutoMutEv:Mutating residue number 15 from chain L (valine) into methionine            (00:02:06)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into asparagine            (00:02:09)
[INFO]       AutoMutEv:Mutating residue number 9 from chain H (glycine) into aspartic acid         (00:02:09)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into alanine                (00:02:12)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into threonine              (00:02:15)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into methionine             (00:02:18)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into threonine:  
                       Energy difference: 0.2072 kcal/mol, Difference in average score from the    
                       base case: -0.0275                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into alanine:    
                       Energy difference: 0.2336 kcal/mol, Difference in average score from the    
                       base case: -0.0253                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into methionine: 
                       Energy difference: -0.5764 kcal/mol, Difference in average score from the   
                       base case: -0.0116                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 12 from chain H (leucine) into            
                       methionine: Energy difference: 0.3475 kcal/mol, Difference in average score 
                       from the base case: -0.0076                                                 (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       methionine: Energy difference: 0.3532 kcal/mol, Difference in average score 
                       from the base case: -0.0167                                                 (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tryptophan: Energy difference: -0.8729 kcal/mol, Difference in average      
                       score from the base case: -0.0015                                           (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tyrosine: Energy difference: 0.5003 kcal/mol, Difference in average score   
                       from the base case: -0.0066                                                 (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 15 from chain L (valine) into threonine:  
                       Energy difference: 0.6313 kcal/mol, Difference in average score from the    
                       base case: -0.0300                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 15 from chain L (valine) into alanine:    
                       Energy difference: 0.6531 kcal/mol, Difference in average score from the    
                       base case: -0.0273                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 15 from chain L (valine) into methionine: 
                       Energy difference: -0.6003 kcal/mol, Difference in average score from the   
                       base case: -0.0134                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into glutamic    
                       acid: Energy difference: 4.1035 kcal/mol, Difference in average score from  
                       the base case: -0.0155                                                      (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into aspartic    
                       acid: Energy difference: 4.2090 kcal/mol, Difference in average score from  
                       the base case: -0.0147                                                      (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 9 from chain H (glycine) into asparagine: 
                       Energy difference: 2.2780 kcal/mol, Difference in average score from the    
                       base case: -0.0115                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into threonine:   
                       Energy difference: 0.1393 kcal/mol, Difference in average score from the    
                       base case: -0.0159                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into alanine:     
                       Energy difference: 0.0559 kcal/mol, Difference in average score from the    
                       base case: -0.0166                                                          (00:02:29)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into methionine:  
                       Energy difference: -0.5158 kcal/mol, Difference in average score from the   
                       base case: -0.0058                                                          (00:02:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:34)
Show buried residues
Minimal score value
-2.6906
Maximal score value
2.1654
Average score
-0.6035
Total score value
-138.2058
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 -0.9091
2 V H 0.0210
3 Q H -0.3274
4 L H 0.0000
5 V H 0.5046
6 E H 0.0000
7 S H -0.2326
8 G H -0.2074
9 G H 0.5109
11 V H 2.1654
12 L H 1.9942
13 V H 0.1944
14 K H -1.8759
15 P H -2.0489
16 G H -1.5358
17 G H -1.2964
18 S H -1.0604
19 L H -0.6084
20 R H -1.4410
21 L H 0.0000
22 S H -0.2571
23 C H 0.0000
24 A H -0.1264
25 A H -0.0688
26 S H -0.0598
27 G H -0.1120
28 F H 1.0640
29 T H 0.3361
30 F H 0.0000
35 S H -0.9611
36 D H -1.2017
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 -0.5280
44 Q H -0.8457
45 A H 0.0000
46 P H -1.0066
47 G H -1.4636
48 K H -2.1846
49 G H -1.1459
50 L H 0.0000
51 E H -0.6189
52 W H 0.0000
53 V H 0.0000
54 S H 0.0000
55 Y H 0.0000
56 I H 0.0000
57 R H 0.0000
58 S H 0.0000
59 G H -1.4577
62 H H -1.6278
63 G H -1.3342
64 N H -1.0555
65 T H -0.4268
66 F H 0.1491
67 Y H -0.5401
68 A H -1.0768
69 D H -2.3129
70 S H -1.4744
71 V H 0.0000
72 K H -2.0916
74 G H -1.5337
75 R H -1.2468
76 F H 0.0000
77 T H -0.5663
78 I H 0.0000
79 S H -0.3543
80 R H -0.9889
81 D H -1.4614
82 N H -1.7181
83 A H -1.3226
84 K H -2.2506
85 N H -1.5124
86 S H 0.0000
87 L H 0.0000
88 Y H -0.0798
89 L H 0.0000
90 Q H -0.9038
91 L H 0.0000
92 N H -1.2180
93 S H -1.2778
94 L H 0.0000
95 R H -2.6906
96 A H -1.9566
97 E H -2.3521
98 D H 0.0000
99 T H -0.6890
100 A H 0.0000
101 V H -0.0899
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 A H 0.0000
106 R H 0.0000
107 G H 0.0000
108 E H -1.7784
109 R H -2.3623
110 H H -2.1733
111 G H -1.5403
111A H H -1.3993
112A Y H -0.1130
112 E H -0.8543
113 G H 0.0000
114 G H -0.3640
115 M H 0.0000
116 D H -0.9087
117 V H -0.2905
118 W H -0.4509
119 G H 0.0000
120 Q H -1.3515
121 G H -0.8707
122 T H -0.1270
123 T H 0.2310
124 V H 0.0000
125 T H 0.2963
126 V H 0.0000
127 S H -0.9641
128 S H -0.9808
1 D L -2.1074
2 I L 0.0000
3 Q L -2.0001
4 M L 0.0000
5 T L -0.9715
6 Q L 0.0000
7 S L -0.5301
8 P L -0.4255
9 S L -0.6376
10 S L -0.7074
11 L L -0.3898
12 S L -0.6512
13 A L 0.0000
14 S L -0.4617
15 V L 0.6841
16 G L -0.3523
17 D L -1.1979
18 R L -2.2302
19 V L 0.0000
20 T L -0.5276
21 I L 0.1013
22 T L -0.6207
23 C L 0.0000
24 R L -2.5521
25 A L 0.0000
26 S L -1.8261
27 Q L -2.0343
28 G L -1.4319
29 I L 0.0000
36 H L -2.0174
37 H L -1.8474
38 D L -1.2971
39 L L 0.0000
40 G L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.6722
44 Q L 0.0000
45 K L -1.6169
46 P L -1.1927
47 G L -1.6346
48 K L -2.4960
49 A L -1.5112
50 P L 0.0000
51 K L -1.0938
52 R L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L -0.1116
56 A L -0.7195
57 A L 0.0000
65 S L -1.0120
66 R L -1.5649
67 L L -0.4890
68 D L -0.7177
69 S L -0.7129
70 G L -0.5722
71 V L -0.4084
72 P L -0.6835
74 S L -0.8333
75 R L -1.6299
76 F L 0.0000
77 S L -0.7642
78 G L -0.4808
79 S L -0.7793
80 G L -1.1741
83 S L -1.2861
84 G L -1.5576
85 T L -1.8089
86 D L -2.0533
87 F L 0.0000
88 T L -0.5417
89 L L 0.0000
90 T L -0.6587
91 I L 0.0000
92 S L -1.5245
93 S L -1.0841
94 L L 0.0000
95 Q L -0.5792
96 P L -0.6561
97 E L -1.8614
98 D L -0.6753
99 F L -0.2066
100 A L 0.0000
101 T L -0.5838
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 -0.3170
108 N L -1.0141
109 S L -0.3537
114 Y L 0.2684
115 P L -0.3518
116 F L 0.0000
117 T L -0.3318
118 F L 0.2329
119 G L 0.0000
120 P L -0.5118
121 G L 0.0000
122 T L 0.0000
123 K L -1.0231
124 V L 0.0000
125 D L -0.3633
126 I L -0.3039
127 K L -1.3606
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
VM15L -0.6003 -0.0134 View CSV PDB
VM11H -0.5764 -0.0116 View CSV PDB
VM5H -0.5158 -0.0058 View CSV PDB
FW28H -0.8729 -0.0015 View CSV PDB
VA5H 0.0559 -0.0166 View CSV PDB
VT11H 0.2072 -0.0275 View CSV PDB
VT15L 0.6313 -0.03 View CSV PDB
FM28H 0.3532 -0.0167 View CSV PDB
LM12H 0.3475 -0.0076 View CSV PDB
GN9H 2.278 -0.0115 View CSV PDB
GE9H 4.1035 -0.0155 View CSV PDB