Project name: Lenvervimab_Charged

Status: done

Started: 2026-07-13 19:08:50
Chain sequence(s) H: EVQLVESGGGLVKPGGSLRLSCSASGFSLTKYKMTWVRQAPGKGLEWVSSISSTSRDIDYADSVKGRFTISRDNAKNSLFLQMSSLRVDDTAVYYCTRDGWLWGWDVRSNYYYNALDVWGQGTTVTVSS
L: DIVVTQSPSSLSASVGDRVTITCRASQGIYNSIAWYQQKPGKAPKLLLYSTSTLLSGVPSRFSGSGSGTDYTLTITNLQPEDFATYYCQQYFVTPETFGQGTKLEIK
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]                                                (00:00:05)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:05)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:05)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:05)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:05)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:24)
[INFO]       AutoMut:  Residue number 112A from chain H and a score of 1.807 (tyrosine) selected   
                       for automated mutation                                                      (00:02:26)
[INFO]       AutoMut:  Residue number 108 from chain L and a score of 1.512 (phenylalanine)        
                       selected for automated mutation                                             (00:02:26)
[INFO]       AutoMut:  Residue number 110 from chain H and a score of 1.423 (leucine) selected for 
                       automated mutation                                                          (00:02:26)
[INFO]       AutoMut:  Residue number 109 from chain L and a score of 1.324 (valine) selected for  
                       automated mutation                                                          (00:02:26)
[INFO]       AutoMut:  Residue number 117 from chain H and a score of 1.314 (valine) selected for  
                       automated mutation                                                          (00:02:26)
[INFO]       AutoMut:  Residue number 112B from chain H and a score of 1.152 (tyrosine) selected   
                       for automated mutation                                                      (00:02:26)
[INFO]       AutoMut:  Mutating residue number 112A from chain H (tyrosine) into glutamic acid     (00:02:26)
[INFO]       AutoMut:  Mutating residue number 112A from chain H (tyrosine) into aspartic acid     (00:02:26)
[INFO]       AutoMut:  Mutating residue number 108 from chain L (phenylalanine) into glutamic acid 
                       Mutating residue number 108 from chain L (phenylalanine) into glutamic acid (00:02:26)
[WARNING]    AutoMut:  Mutation YE112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YE112AH/Aggrescan.error       (00:02:28)
[INFO]       AutoMut:  Mutating residue number 112A from chain H (tyrosine) into lysine            (00:02:28)
[WARNING]    AutoMut:  Mutation YD112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YD112AH/Aggrescan.error       (00:02:28)
[INFO]       AutoMut:  Mutating residue number 112A from chain H (tyrosine) into arginine          (00:02:28)
[WARNING]    AutoMut:  Mutation YK112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YK112AH/Aggrescan.error       (00:02:30)
[INFO]       AutoMut:  Mutating residue number 108 from chain L (phenylalanine) into aspartic acid 
                       Mutating residue number 108 from chain L (phenylalanine) into aspartic acid (00:02:30)
[WARNING]    AutoMut:  Mutation YR112AH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YR112AH/Aggrescan.error       (00:02:30)
[INFO]       AutoMut:  Mutating residue number 110 from chain H (leucine) into glutamic acid       (00:02:30)
[INFO]       AutoMut:  Mutating residue number 108 from chain L (phenylalanine) into lysine        (00:02:39)
[INFO]       AutoMut:  Mutating residue number 108 from chain L (phenylalanine) into arginine      (00:02:42)
[INFO]       AutoMut:  Mutating residue number 110 from chain H (leucine) into lysine              (00:02:50)
[INFO]       AutoMut:  Mutating residue number 110 from chain H (leucine) into aspartic acid       (00:02:56)
[INFO]       AutoMut:  Mutating residue number 109 from chain L (valine) into glutamic acid        (00:02:58)
[INFO]       AutoMut:  Mutating residue number 109 from chain L (valine) into lysine               (00:03:08)
[INFO]       AutoMut:  Mutating residue number 110 from chain H (leucine) into arginine            (00:03:13)
[INFO]       AutoMut:  Mutating residue number 109 from chain L (valine) into aspartic acid        (00:03:18)
[INFO]       AutoMut:  Mutating residue number 109 from chain L (valine) into arginine             (00:03:26)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (valine) into glutamic acid        (00:03:26)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (valine) into aspartic acid        (00:03:34)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (valine) into lysine               (00:03:38)
[INFO]       AutoMut:  Mutating residue number 117 from chain H (valine) into arginine             (00:03:43)
[INFO]       AutoMut:  Mutating residue number 112B from chain H (tyrosine) into glutamic acid     (00:03:44)
[WARNING]    AutoMut:  Mutation YE112BH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YE112BH/Aggrescan.error       (00:03:46)
[INFO]       AutoMut:  Mutating residue number 112B from chain H (tyrosine) into lysine            (00:03:46)
[WARNING]    AutoMut:  Mutation YK112BH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YK112BH/Aggrescan.error       (00:03:48)
[INFO]       AutoMut:  Mutating residue number 112B from chain H (tyrosine) into aspartic acid     (00:03:48)
[WARNING]    AutoMut:  Mutation YD112BH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YD112BH/Aggrescan.error       (00:03:49)
[INFO]       AutoMut:  Mutating residue number 112B from chain H (tyrosine) into arginine          (00:03:49)
[WARNING]    AutoMut:  Mutation YR112BH could have failed (this can be ignored if the main program 
                       reports the energy difference). Simulation log for that run should be       
                       available at                                                                
                       /STORAGE/DATA/lcbio/aggreskan/58fb02e25a10805/YR112BH/Aggrescan.error       (00:03:52)
[INFO]       AutoMut:  Effect of mutation residue number 108 from chain L (phenylalanine) into     
                       glutamic acid: Energy difference: 0.9650 kcal/mol, Difference in average    
                       score from the base case: -0.0319                                           (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 108 from chain L (phenylalanine) into     
                       lysine: Energy difference: -0.3605 kcal/mol, Difference in average score    
                       from the base case: -0.0257                                                 (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 108 from chain L (phenylalanine) into     
                       aspartic acid: Energy difference: 1.4019 kcal/mol, Difference in average    
                       score from the base case: -0.0353                                           (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 108 from chain L (phenylalanine) into     
                       arginine: Energy difference: -0.1184 kcal/mol, Difference in average score  
                       from the base case: -0.0350                                                 (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 110 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.7782 kcal/mol, Difference in average score from  
                       the base case: -0.0385                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 110 from chain H (leucine) into lysine:   
                       Energy difference: 0.8108 kcal/mol, Difference in average score from the    
                       base case: -0.0377                                                          (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 110 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.2916 kcal/mol, Difference in average score from  
                       the base case: -0.0422                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 110 from chain H (leucine) into arginine: 
                       Energy difference: 1.1990 kcal/mol, Difference in average score from the    
                       base case: -0.0404                                                          (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 109 from chain L (valine) into glutamic   
                       acid: Energy difference: 0.2659 kcal/mol, Difference in average score from  
                       the base case: -0.0381                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 109 from chain L (valine) into lysine:    
                       Energy difference: -0.5647 kcal/mol, Difference in average score from the   
                       base case: -0.0413                                                          (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 109 from chain L (valine) into aspartic   
                       acid: Energy difference: 0.5789 kcal/mol, Difference in average score from  
                       the base case: -0.0406                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 109 from chain L (valine) into arginine:  
                       Energy difference: -0.7170 kcal/mol, Difference in average score from the   
                       base case: -0.0377                                                          (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (valine) into glutamic   
                       acid: Energy difference: -0.0030 kcal/mol, Difference in average score from 
                       the base case: -0.0461                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (valine) into lysine:    
                       Energy difference: -0.7747 kcal/mol, Difference in average score from the   
                       base case: -0.0386                                                          (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (valine) into aspartic   
                       acid: Energy difference: 0.0025 kcal/mol, Difference in average score from  
                       the base case: -0.0407                                                      (00:04:12)
[INFO]       AutoMut:  Effect of mutation residue number 117 from chain H (valine) into arginine:  
                       Energy difference: -0.7371 kcal/mol, Difference in average score from the   
                       base case: -0.0406                                                          (00:04:12)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:18)
Show buried residues
Minimal score value
-3.0774
Maximal score value
1.8069
Average score
-0.4785
Total score value
-112.9266
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 E H -1.5007
2 V H -0.0969
3 Q H -0.3322
4 L H 0.0000
5 V H 0.1397
6 E H 0.0000
7 S H -0.6845
8 G H -1.1198
9 G H -0.4878
11 G H 0.1463
12 L H 1.1072
13 V H 0.0845
14 K H -1.6342
15 P H -1.2360
16 G H -1.4495
17 G H -1.2881
18 S H -1.3918
19 L H 0.0000
20 R H -2.1887
21 L H 0.0000
22 S H -0.6193
23 C H 0.0000
24 S H -0.5961
25 A H 0.0000
26 S H -0.5346
27 G H -0.4067
28 F H 1.0244
29 S H 0.3051
30 L H 0.0000
35 T H -0.5650
36 K H -0.5366
37 Y H -0.0421
38 K H 0.0000
39 M H 0.0000
40 T H 0.0000
41 W H 0.0000
42 V H 0.0000
43 R H 0.0000
44 Q H -0.8168
45 A H -0.9902
46 P H -0.9343
47 G H -1.4286
48 K H -2.3648
49 G H -1.6108
50 L H 0.0000
51 E H -1.2334
52 W H 0.0000
53 V H 0.0000
54 S H 0.0000
55 S H 0.0000
56 I H 0.0000
57 S H 0.0000
58 S H 0.0000
59 T H -0.9639
62 S H -1.1784
63 R H -2.1713
64 D H -1.4144
65 I H -0.5796
66 D H -0.7993
67 Y H -1.2156
68 A H -1.6510
69 D H -2.9779
70 S H -1.7878
71 V H 0.0000
72 K H -3.0774
74 G H -2.4555
75 R H -2.9058
76 F H 0.0000
77 T H -1.1914
78 I H 0.0000
79 S H -0.5809
80 R H -1.0825
81 D H -1.3194
82 N H -1.4593
83 A H -1.2052
84 K H -2.1840
85 N H -1.4444
86 S H -1.0409
87 L H 0.0000
88 F H -0.5548
89 L H 0.0000
90 Q H -1.6111
91 M H 0.0000
92 S H -1.4453
93 S H -1.6867
94 L H 0.0000
95 R H -1.9916
96 V H -0.2354
97 D H -1.5999
98 D H 0.0000
99 T H -0.1109
100 A H 0.0000
101 V H 0.2349
102 Y H 0.0000
103 Y H 0.0000
104 C H 0.0000
105 T H 0.0000
106 R H 0.0000
107 D H 0.0000
108 G H 0.1264
109 W H 0.0000
110 L H 1.4234
111 W H 0.0000
111A G H 0.1481
111B W H 0.7500
111C D H -0.9066
111D V H 0.7337
112E R H -0.5000
112D S H 0.0918
112C N H 0.3137
112B Y H 1.1516
112A Y H 1.8069
112 Y H 0.0000
113 N H 0.4296
114 A H 0.0000
115 L H 0.0000
116 D H 0.4273
117 V H 1.3136
118 W H 0.4998
119 G H -0.3219
120 Q H -1.1833
121 G H -0.6398
122 T H -0.3602
123 T H 0.0583
124 V H 0.0000
125 T H 0.2704
126 V H 0.0000
127 S H -0.2987
128 S H -0.5136
1 D L -1.5446
2 I L 0.0017
3 V L 0.9473
4 V L 0.0000
5 T L -0.4558
6 Q L -0.9174
7 S L -0.6853
8 P L -0.7101
9 S L -1.0305
10 S L -1.0831
11 L L -0.6319
12 S L -1.0099
13 A L 0.0000
14 S L -1.0822
15 V L -0.1031
16 G L -1.1322
17 D L -1.8911
18 R L -2.2553
19 V L 0.0000
20 T L -0.4985
21 I L 0.0000
22 T L -0.7593
23 C L 0.0000
24 R L -1.9475
25 A L 0.0000
26 S L -1.0072
27 Q L -1.6488
28 G L -0.9634
29 I L 0.0000
36 Y L 0.3068
37 N L -0.5015
38 S L 0.1364
39 I L 0.0000
40 A L 0.0000
41 W L 0.0000
42 Y L 0.0000
43 Q L 0.0000
44 Q L 0.0000
45 K L -1.5119
46 P L -1.0474
47 G L -1.3371
48 K L -1.9881
49 A L -0.9843
50 P L 0.0000
51 K L -0.4684
52 L L 0.3021
53 L L 0.0000
54 L L 0.0000
55 Y L 0.3003
56 S L -0.0608
57 T L 0.0000
65 S L -0.2584
66 T L 0.2653
67 L L 0.5610
68 L L 0.3189
69 S L -0.1813
70 G L -0.4743
71 V L 0.0000
72 P L -0.4987
74 S L -0.6183
75 R L -1.2592
76 F L 0.0000
77 S L -0.3464
78 G L -0.1561
79 S L -0.7077
80 G L -1.0328
83 S L -0.8228
84 G L -0.9355
85 T L -1.6852
86 D L -2.2973
87 Y L 0.0000
88 T L -0.7070
89 L L 0.0000
90 T L -0.6000
91 I L 0.0000
92 T L -1.5965
93 N L -1.8710
94 L L 0.0000
95 Q L -0.8165
96 P L -0.8238
97 E L -1.7779
98 D L 0.0000
99 F L -0.2622
100 A L 0.0000
101 T L -0.9420
102 Y L 0.0000
103 Y L 0.0000
104 C L 0.0000
105 Q L 0.0000
106 Q L 0.0000
107 Y L 0.9900
108 F L 1.5117
109 V L 1.3237
114 T L 0.2909
115 P L -0.3567
116 E L 0.0000
117 T L 0.0014
118 F L 0.0000
119 G L 0.0000
120 Q L -1.7257
121 G L 0.0000
122 T L 0.0000
123 K L -1.8007
124 L L 0.0000
125 E L -1.5767
126 I L -0.9596
127 K L -1.6886
Download PDB file
View in 3Dmol

Automated mutations analysis - charged mutations

In the automated mutations mode, the server selects aggregation prone resides and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine. 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
VR117H -0.7371 -0.0406 View CSV PDB
VK117H -0.7747 -0.0386 View CSV PDB
VR109L -0.717 -0.0377 View CSV PDB
VK109L -0.5647 -0.0413 View CSV PDB
FK108L -0.3605 -0.0257 View CSV PDB
FR108L -0.1184 -0.035 View CSV PDB
LD110H 0.2916 -0.0422 View CSV PDB
LE110H 0.7782 -0.0385 View CSV PDB