Project name: 00256

Status: done

Started: 2025-08-01 20:42:22
Chain sequence(s) H: QVQLVESGGVLVKPGGSLRLSCAASGFTFSDYYMSWIRQAPGKGLEWVSHIRSGGGHTFYADSVKGRFTISRDNAKNSLYLQLNSLRAEDTAVYYCARGERTGDYTGGMDVWGQGTTVTVSS
L: DIQMTQSPSSLSASVGDRVTITCRASEGIHHDLGWYQQKPGKAPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHHSYPFTFGPGTKVDIK
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                                          (00:01:27)
[INFO]       AutoMutEv:Residue number 11 from chain H and a score of 2.133 (valine) selected for   
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Residue number 12 from chain H and a score of 1.988 (leucine) selected for  
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Residue number 5 from chain H and a score of 1.198 (valine) selected for    
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Residue number 28 from chain H and a score of 1.155 (phenylalanine)         
                       selected for automated mutation                                             (00:01:29)
[INFO]       AutoMutEv:Residue number 55 from chain L and a score of 0.495 (tyrosine) selected for 
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Residue number 99 from chain L and a score of 0.492 (phenylalanine)         
                       selected for automated mutation                                             (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into methionine            (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into threonine             (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into threonine              (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 11 from chain H (valine) into alanine               (00:01:34)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into alanine                (00:01:35)
[INFO]       AutoMutEv:Mutating residue number 12 from chain H (leucine) into methionine           (00:01:36)
[INFO]       AutoMutEv:Mutating residue number 5 from chain H (valine) into methionine             (00:01:40)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tryptophan     (00:01:42)
[INFO]       AutoMutEv:Mutating residue number 55 from chain L (tyrosine) into histidine           (00:01:43)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into methionine     (00:01:50)
[INFO]       AutoMutEv:Mutating residue number 28 from chain H (phenylalanine) into tyrosine       (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 55 from chain L (tyrosine) into cysteine            (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 55 from chain L (tyrosine) into tryptophan          (00:01:58)
[INFO]       AutoMutEv:Mutating residue number 99 from chain L (phenylalanine) into tryptophan     (00:01:59)
[INFO]       AutoMutEv:Mutating residue number 99 from chain L (phenylalanine) into methionine     (00:02:07)
[INFO]       AutoMutEv:Mutating residue number 99 from chain L (phenylalanine) into tyrosine       (00:02:12)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into threonine:  
                       Energy difference: -0.0658 kcal/mol, Difference in average score from the   
                       base case: -0.0275                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into alanine:    
                       Energy difference: 0.3691 kcal/mol, Difference in average score from the    
                       base case: -0.0252                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain H (valine) into methionine: 
                       Energy difference: -0.3430 kcal/mol, Difference in average score from the   
                       base case: -0.0111                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 12 from chain H (leucine) into            
                       methionine: Energy difference: 0.1118 kcal/mol, Difference in average score 
                       from the base case: -0.0074                                                 (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into threonine:   
                       Energy difference: 0.0292 kcal/mol, Difference in average score from the    
                       base case: -0.0244                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into alanine:     
                       Energy difference: 0.1776 kcal/mol, Difference in average score from the    
                       base case: -0.0302                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain H (valine) into methionine:  
                       Energy difference: -0.3337 kcal/mol, Difference in average score from the   
                       base case: -0.0152                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       methionine: Energy difference: -0.2038 kcal/mol, Difference in average      
                       score from the base case: -0.0180                                           (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tryptophan: Energy difference: -0.4904 kcal/mol, Difference in average      
                       score from the base case: -0.0123                                           (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 28 from chain H (phenylalanine) into      
                       tyrosine: Energy difference: 0.2612 kcal/mol, Difference in average score   
                       from the base case: -0.0097                                                 (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 55 from chain L (tyrosine) into           
                       histidine: Energy difference: 1.0835 kcal/mol, Difference in average score  
                       from the base case: -0.0109                                                 (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 55 from chain L (tyrosine) into cysteine: 
                       Energy difference: 1.2244 kcal/mol, Difference in average score from the    
                       base case: -0.0054                                                          (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 55 from chain L (tyrosine) into           
                       tryptophan: Energy difference: 0.3876 kcal/mol, Difference in average score 
                       from the base case: -0.0002                                                 (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 99 from chain L (phenylalanine) into      
                       methionine: Energy difference: -0.3999 kcal/mol, Difference in average      
                       score from the base case: -0.0151                                           (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 99 from chain L (phenylalanine) into      
                       tryptophan: Energy difference: 0.1877 kcal/mol, Difference in average score 
                       from the base case: -0.0089                                                 (00:02:20)
[INFO]       AutoMutEv:Effect of mutation residue number 99 from chain L (phenylalanine) into      
                       tyrosine: Energy difference: 0.0271 kcal/mol, Difference in average score   
                       from the base case: -0.0051                                                 (00:02:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:25)
Show buried residues
Minimal score value
-2.9881
Maximal score value
2.133
Average score
-0.6294
Total score value
-144.1225
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 -0.8634
2 V H 0.0816
3 Q H -0.1994
4 L H 0.0000
5 V H 1.1982
6 E H 0.0000
7 S H -0.1653
8 G H -0.3556
9 G H 0.4647
11 V H 2.1330
12 L H 1.9881
13 V H 0.1419
14 K H -1.9158
15 P H -1.9480
16 G H -1.5644
17 G H -1.3186
18 S H -1.1255
19 L H -0.7614
20 R H -1.8156
21 L H 0.0000
22 S H -0.3035
23 C H 0.0000
24 A H 0.0666
25 A H 0.0000
26 S H -0.1310
27 G H -0.0688
28 F H 1.1546
29 T H 0.1633
30 F H 0.0000
35 S H -1.5779
36 D H -2.2114
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 -0.6003
45 A H -0.9242
46 P H -0.7992
47 G H -1.1437
48 K H -1.3386
49 G H -0.8712
50 L H 0.0000
51 E H -0.3370
52 W H 0.1368
53 V H 0.0000
54 S H 0.0000
55 H H 0.0000
56 I H 0.0000
57 R H -1.7676
58 S H -1.9435
59 G H -1.7377
62 G H -1.2361
63 G H -1.3538
64 H H -1.4693
65 T H -0.7333
66 F H -0.2710
67 Y H -0.5190
68 A H -1.1542
69 D H -2.4169
70 S H -1.7356
71 V H 0.0000
72 K H -2.4627
74 G H -1.7148
75 R H -1.3258
76 F H 0.0000
77 T H -0.6494
78 I H 0.0000
79 S H -0.3933
80 R H -1.4046
81 D H -2.0974
82 N H -2.6501
83 A H -1.7542
84 K H -2.4849
85 N H -1.7971
86 S H 0.0000
87 L H 0.0000
88 Y H -0.3474
89 L H 0.0000
90 Q H -1.0312
91 L H 0.0000
92 N H -1.2385
93 S H -1.3276
94 L H 0.0000
95 R H -2.9069
96 A H -1.9916
97 E H -2.4444
98 D H 0.0000
99 T H -0.7568
100 A H 0.0000
101 V H -0.1531
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 -1.7750
109 R H -1.5996
110 T H -1.0837
111 G H -1.3317
111A D H -2.0427
112A Y H -0.9643
112 T H -0.8665
113 G H 0.0000
114 G H 0.0000
115 M H 0.0000
116 D H -0.8109
117 V H -0.2052
118 W H -0.1176
119 G H 0.0000
120 Q H -1.1656
121 G H -0.6930
122 T H -0.0145
123 T H 0.3082
124 V H 0.0000
125 T H 0.2249
126 V H 0.0000
127 S H -0.8583
128 S H -1.0060
1 D L -2.3132
2 I L 0.0000
3 Q L -2.2461
4 M L 0.0000
5 T L -0.9840
6 Q L 0.0000
7 S L -0.5715
8 P L -0.4991
9 S L -0.6703
10 S L -0.7198
11 L L -0.3865
12 S L -0.7234
13 A L 0.0000
14 S L -0.7678
15 V L 0.1464
16 G L -0.7745
17 D L -1.6242
18 R L -2.3442
19 V L 0.0000
20 T L -0.6444
21 I L 0.0000
22 T L -0.8933
23 C L 0.0000
24 R L -2.8905
25 A L -2.3442
26 S L -2.3986
27 E L -2.9881
28 G L -2.1394
29 I L 0.0000
36 H L -2.2743
37 H L -1.8942
38 D L 0.0000
39 L L 0.0000
40 G L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L -0.4023
44 Q L 0.0000
45 K L -1.3356
46 P L -1.0817
47 G L -1.6833
48 K L -2.3789
49 A L -1.3143
50 P L 0.0000
51 K L -0.7286
52 R L 0.0000
53 L L 0.0000
54 I L 0.0000
55 Y L 0.4954
56 A L -0.3175
57 A L 0.0000
65 S L -0.1989
66 S L 0.1952
67 L L 0.4132
68 Q L 0.0000
69 S L -0.3692
70 G L -0.4638
71 V L -0.2787
72 P L -0.4896
74 S L -0.6351
75 R L -1.1662
76 F L 0.0000
77 S L -0.4073
78 G L -0.1526
79 S L -0.6799
80 G L -1.4080
83 S L -1.5126
84 G L -1.9088
85 T L -2.4677
86 E L -2.8966
87 F L 0.0000
88 T L -0.8063
89 L L 0.0000
90 T L -0.6566
91 I L 0.0000
92 S L -1.4090
93 S L -1.2070
94 L L 0.0000
95 Q L -0.5476
96 P L -0.5509
97 E L -1.4084
98 D L 0.0000
99 F L 0.4917
100 A L 0.0000
101 T L -0.4364
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 H L -1.4301
109 S L -0.4408
114 Y L 0.2325
115 P L -0.1653
116 F L -0.0346
117 T L -0.2599
118 F L 0.1178
119 G L 0.0000
120 P L -0.4286
121 G L 0.0000
122 T L 0.0000
123 K L -0.9077
124 V L 0.0000
125 D L -0.2456
126 I L -0.4248
127 K L -1.4040
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
VT11H -0.0658 -0.0275 View CSV PDB
FM99L -0.3999 -0.0151 View CSV PDB
VM5H -0.3337 -0.0152 View CSV PDB
FM28H -0.2038 -0.018 View CSV PDB
FW28H -0.4904 -0.0123 View CSV PDB
VM11H -0.343 -0.0111 View CSV PDB
VT5H 0.0292 -0.0244 View CSV PDB
FY99L 0.0271 -0.0051 View CSV PDB
LM12H 0.1118 -0.0074 View CSV PDB
YH55L 1.0835 -0.0109 View CSV PDB
YC55L 1.2244 -0.0054 View CSV PDB