Project name: aTfR_BF2_VHH_new

Status: done

Started: 2025-11-16 16:15:19
Settings
Chain sequence(s) H: QVQLQESGGGLVQAGGSLRLSCAASGYISKYRFMGWYRQAPGKEREFVAGISRGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAALLIGAGDSDDLLYYWGQGTQVTVSS
input PDB
Selected Chain(s) H
Distance of aggregation 5 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with H chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:02)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:01:34)
[INFO]       Auto_mut: Residue number 64 from chain H and a score of 1.970 (isoleucine) selected   
                       for automated muatation                                                     (00:01:36)
[INFO]       Auto_mut: Residue number 12 from chain H and a score of 1.556 omitted from automated  
                       muatation (excluded by the user).                                           (00:01:36)
[INFO]       Auto_mut: Residue number 114 from chain H and a score of 1.358 (leucine) selected for 
                       automated muatation                                                         (00:01:36)
[INFO]       Auto_mut: Residue number 28 from chain H and a score of 1.295 omitted from automated  
                       muatation (excluded by the user).                                           (00:01:36)
[INFO]       Auto_mut: Residue number 116 from chain H and a score of 1.141 (tyrosine) selected    
                       for automated muatation                                                     (00:01:36)
[INFO]       Auto_mut: Residue number 66 from chain H and a score of 1.015 (tyrosine) selected for 
                       automated muatation                                                         (00:01:36)
[INFO]       Auto_mut: Residue number 52 from chain H and a score of 0.831 (phenylalanine)         
                       selected for automated muatation                                            (00:01:36)
[INFO]       Auto_mut: Residue number 38 from chain H and a score of 0.523 (phenylalanine)         
                       selected for automated muatation                                            (00:01:36)
[INFO]       Auto_mut: Mutating residue number 64 from chain H (isoleucine) into glutamic acid     (00:01:36)
[INFO]       Auto_mut: Mutating residue number 64 from chain H (isoleucine) into aspartic acid     (00:01:36)
[INFO]       Auto_mut: Mutating residue number 114 from chain H (leucine) into glutamic acid       (00:01:36)
[INFO]       Auto_mut: Mutating residue number 64 from chain H (isoleucine) into arginine          (00:02:52)
[INFO]       Auto_mut: Mutating residue number 114 from chain H (leucine) into lysine              (00:02:57)
[INFO]       Auto_mut: Mutating residue number 64 from chain H (isoleucine) into lysine            (00:03:02)
[INFO]       Auto_mut: Mutating residue number 114 from chain H (leucine) into aspartic acid       (00:04:14)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (tyrosine) into glutamic acid      (00:04:29)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (tyrosine) into aspartic acid      (00:04:32)
[INFO]       Auto_mut: Mutating residue number 114 from chain H (leucine) into arginine            (00:05:30)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (tyrosine) into lysine             (00:05:53)
[INFO]       Auto_mut: Mutating residue number 116 from chain H (tyrosine) into arginine           (00:05:54)
[INFO]       Auto_mut: Mutating residue number 66 from chain H (tyrosine) into glutamic acid       (00:06:47)
[INFO]       Auto_mut: Mutating residue number 66 from chain H (tyrosine) into aspartic acid       (00:07:17)
[INFO]       Auto_mut: Mutating residue number 52 from chain H (phenylalanine) into glutamic acid  
                       Mutating residue number 52 from chain H (phenylalanine) into glutamic acid  (00:07:27)
[INFO]       Auto_mut: Mutating residue number 66 from chain H (tyrosine) into lysine              (00:08:16)
[INFO]       Auto_mut: Mutating residue number 66 from chain H (tyrosine) into arginine            (00:08:30)
[INFO]       Auto_mut: Mutating residue number 52 from chain H (phenylalanine) into lysine         (00:08:42)
[INFO]       Auto_mut: Mutating residue number 52 from chain H (phenylalanine) into aspartic acid  
                       Mutating residue number 52 from chain H (phenylalanine) into aspartic acid  (00:09:50)
[INFO]       Auto_mut: Mutating residue number 38 from chain H (phenylalanine) into glutamic acid  
                       Mutating residue number 38 from chain H (phenylalanine) into glutamic acid  (00:09:59)
[INFO]       Auto_mut: Mutating residue number 38 from chain H (phenylalanine) into aspartic acid  
                       Mutating residue number 38 from chain H (phenylalanine) into aspartic acid  (00:10:02)
[INFO]       Auto_mut: Mutating residue number 52 from chain H (phenylalanine) into arginine       (00:11:08)
[INFO]       Auto_mut: Mutating residue number 38 from chain H (phenylalanine) into arginine       (00:11:13)
[INFO]       Auto_mut: Mutating residue number 38 from chain H (phenylalanine) into lysine         (00:11:14)
[INFO]       Auto_mut: Effect of mutation residue number 64 from chain H (isoleucine) into         
                       glutamic acid: Energy difference: -0.2190 kcal/mol, Difference in average   
                       score from the base case: -0.0448                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 64 from chain H (isoleucine) into lysine: 
                       Energy difference: -0.3940 kcal/mol, Difference in average score from the   
                       base case: -0.0442                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 64 from chain H (isoleucine) into         
                       aspartic acid: Energy difference: -0.8727 kcal/mol, Difference in average   
                       score from the base case: -0.0397                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 64 from chain H (isoleucine) into         
                       arginine: Energy difference: -0.3429 kcal/mol, Difference in average score  
                       from the base case: -0.0454                                                 (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 114 from chain H (leucine) into glutamic  
                       acid: Energy difference: 0.3727 kcal/mol, Difference in average score from  
                       the base case: -0.0338                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 114 from chain H (leucine) into lysine:   
                       Energy difference: -0.1620 kcal/mol, Difference in average score from the   
                       base case: -0.0343                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 114 from chain H (leucine) into aspartic  
                       acid: Energy difference: 0.3160 kcal/mol, Difference in average score from  
                       the base case: -0.0331                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 114 from chain H (leucine) into arginine: 
                       Energy difference: 0.0262 kcal/mol, Difference in average score from the    
                       base case: -0.0341                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (tyrosine) into glutamic 
                       acid: Energy difference: 0.7031 kcal/mol, Difference in average score from  
                       the base case: -0.0267                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (tyrosine) into lysine:  
                       Energy difference: -1.1645 kcal/mol, Difference in average score from the   
                       base case: -0.0195                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (tyrosine) into aspartic 
                       acid: Energy difference: 0.9291 kcal/mol, Difference in average score from  
                       the base case: -0.0245                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 116 from chain H (tyrosine) into          
                       arginine: Energy difference: -1.8310 kcal/mol, Difference in average score  
                       from the base case: -0.0117                                                 (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain H (tyrosine) into glutamic  
                       acid: Energy difference: 0.4588 kcal/mol, Difference in average score from  
                       the base case: -0.0365                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain H (tyrosine) into lysine:   
                       Energy difference: 0.5266 kcal/mol, Difference in average score from the    
                       base case: -0.0232                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain H (tyrosine) into aspartic  
                       acid: Energy difference: 0.8943 kcal/mol, Difference in average score from  
                       the base case: -0.0358                                                      (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 66 from chain H (tyrosine) into arginine: 
                       Energy difference: 0.6923 kcal/mol, Difference in average score from the    
                       base case: -0.0402                                                          (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain H (phenylalanine) into      
                       glutamic acid: Energy difference: 1.0987 kcal/mol, Difference in average    
                       score from the base case: -0.0278                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain H (phenylalanine) into      
                       lysine: Energy difference: 0.5314 kcal/mol, Difference in average score     
                       from the base case: -0.0211                                                 (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain H (phenylalanine) into      
                       aspartic acid: Energy difference: 1.1320 kcal/mol, Difference in average    
                       score from the base case: -0.0237                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 52 from chain H (phenylalanine) into      
                       arginine: Energy difference: 0.2690 kcal/mol, Difference in average score   
                       from the base case: -0.0295                                                 (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 38 from chain H (phenylalanine) into      
                       glutamic acid: Energy difference: 0.9692 kcal/mol, Difference in average    
                       score from the base case: -0.0243                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 38 from chain H (phenylalanine) into      
                       lysine: Energy difference: 0.6427 kcal/mol, Difference in average score     
                       from the base case: -0.0257                                                 (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 38 from chain H (phenylalanine) into      
                       aspartic acid: Energy difference: 2.6021 kcal/mol, Difference in average    
                       score from the base case: -0.0140                                           (00:12:58)
[INFO]       Auto_mut: Effect of mutation residue number 38 from chain H (phenylalanine) into      
                       arginine: Energy difference: -0.4025 kcal/mol, Difference in average score  
                       from the base case: -0.0270                                                 (00:12:58)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:04)
Show buried residues
Minimal score value
-2.1224
Maximal score value
1.9698
Average score
-0.2941
Total score value
-35.8854
Download the table (csv)

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 Q H -1.1669
2 V H -0.2611
3 Q H -1.1667
4 L H 0.0000
5 Q H -1.1983
6 E H 0.0000
7 S H -0.1980
8 G H -0.4769
9 G H -0.2991
11 G H 0.0102
12 L H 1.5555
13 V H 0.3584
14 Q H -1.1489
15 A H -0.2666
16 G H -0.5084
17 G H -0.2285
18 S H -0.1966
19 L H -0.0914
20 R H -1.7700
21 L H 0.0000
22 S H -0.0163
23 C H 0.0000
24 A H 0.0330
25 A H -0.0250
26 S H -0.2314
27 G H 0.0952
28 Y H 1.2949
29 I H 0.0000
30 S H -0.5121
35 K H -1.7375
36 Y H 0.0000
37 R H -0.9893
38 F H 0.5227
39 M H 0.0000
40 G H 0.0000
41 W H 0.0000
42 Y H 0.3288
43 R H 0.0000
44 Q H -0.6213
45 A H -0.1340
46 P H -0.3374
47 G H -0.6757
48 K H -1.3492
49 E H -2.1224
50 R H -1.1868
51 E H -0.3026
52 F H 0.8309
53 V H 0.0000
54 A H 0.0000
55 G H 0.0000
56 I H 0.0000
57 S H 0.0000
58 R H -2.0224
59 G H -0.8327
63 S H 0.0637
64 I H 1.9698
65 T H 0.5124
66 Y H 1.0148
67 Y H 0.4413
68 A H -0.2568
69 D H -2.0098
70 S H -0.5304
71 V H 0.0000
72 K H -1.9787
74 G H -0.8403
75 R H -0.4688
76 F H 0.0000
77 T H -0.0511
78 I H 0.0000
79 S H -0.1795
80 R H -0.3675
81 D H -1.0190
82 N H -1.4199
83 A H -0.4695
84 K H -1.7232
85 N H -0.6310
86 T H 0.0000
87 V H 0.0000
88 Y H 0.1616
89 L H 0.0000
90 Q H -0.6440
91 M H 0.0000
92 N H -0.5703
93 S H -0.3479
94 L H 0.0000
95 K H -1.4014
96 P H -0.6874
97 E H -1.8410
98 D H 0.0000
99 T H -0.0161
100 A H 0.0000
101 V H 0.3549
102 Y H 0.0000
103 Y H 0.2172
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 L H 0.3680
108 L H 0.3849
109 I H 0.0000
110 G H -0.3959
111 A H -0.1067
111A G H -0.7821
112B D H -1.9132
112A S H -0.9994
112 D H -1.9073
113 D H -1.1215
114 L H 1.3576
115 L H 0.0000
116 Y H 1.1413
117 Y H 0.4120
118 W H 0.3326
119 G H -0.2174
120 Q H -1.2233
121 G H -0.2639
122 T H -0.1613
123 Q H -0.6924
124 V H 0.0000
125 T H 0.1585
126 V H 0.0000
127 S H -0.2642
128 S H -0.2299
Download PDB file
View in 3Dmol
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Automated mutations analysis

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
ID64H -0.8727 -0.0397 View CSV PDB
IK64H -0.394 -0.0442 View CSV PDB
YK116H -1.1645 -0.0195 View CSV PDB
YR116H -1.831 -0.0117 View CSV PDB
FR38H -0.4025 -0.027 View CSV PDB
LK114H -0.162 -0.0343 View CSV PDB
LR114H 0.0262 -0.0341 View CSV PDB
FR52H 0.269 -0.0295 View CSV PDB
YE66H 0.4588 -0.0365 View CSV PDB
YR66H 0.6923 -0.0402 View CSV PDB
FK38H 0.6427 -0.0257 View CSV PDB
FK52H 0.5314 -0.0211 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018