Project name: fold_rfa148_b3v_a5v_b39s_fv84b_b27vq_b93vc_a11ls

Status: done

Started: 2026-06-25 02:51:20
Chain sequence(s) A: EVQLAESGGGSEQPGGSLRLSCAGSGFTFSSQGFGWVRQAPGKGLEWVSSISADGSGTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARLSRVRVGSTRGVVGDVWGQGTTVTVSS
B: DIAMTQSPLSLPVTPGEPASISCRSSQETSAIGWYLQKPGQSPQLLIYGTSTRGSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCMQGTGCPGTFGQGTKLEIKR
input PDB
Selected Chain(s) A,B
Distance of aggregation 5 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                                          (00:01:36)
[INFO]       AutoMut:  Residue number 9 from chain B and a score of 1.172 (leucine) selected for   
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Residue number 93 from chain B and a score of 0.700 (cysteine) selected for 
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Residue number 48 from chain B and a score of 0.510 (tyrosine) selected for 
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Residue number 93 from chain A and a score of 0.490 (valine) selected for   
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Residue number 82 from chain B and a score of 0.430 (valine) selected for   
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Residue number 60 from chain A and a score of 0.237 (tyrosine) selected for 
                       automated mutation                                                          (00:01:38)
[INFO]       AutoMut:  Mutating residue number 9 from chain B (leucine) into glutamic acid         (00:01:38)
[INFO]       AutoMut:  Mutating residue number 9 from chain B (leucine) into aspartic acid         (00:01:38)
[INFO]       AutoMut:  Mutating residue number 93 from chain B (cysteine) into glutamic acid       (00:01:38)
[INFO]       AutoMut:  Mutating residue number 9 from chain B (leucine) into arginine              (00:01:45)
[INFO]       AutoMut:  Mutating residue number 9 from chain B (leucine) into lysine                (00:01:45)
[INFO]       AutoMut:  Mutating residue number 93 from chain B (cysteine) into lysine              (00:01:56)
[INFO]       AutoMut:  Mutating residue number 93 from chain B (cysteine) into aspartic acid       (00:01:59)
[INFO]       AutoMut:  Mutating residue number 48 from chain B (tyrosine) into glutamic acid       (00:02:04)
[INFO]       AutoMut:  Mutating residue number 93 from chain B (cysteine) into arginine            (00:02:11)
[INFO]       AutoMut:  Mutating residue number 48 from chain B (tyrosine) into lysine              (00:02:13)
[INFO]       AutoMut:  Mutating residue number 48 from chain B (tyrosine) into aspartic acid       (00:02:16)
[INFO]       AutoMut:  Mutating residue number 48 from chain B (tyrosine) into arginine            (00:02:23)
[INFO]       AutoMut:  Mutating residue number 93 from chain A (valine) into glutamic acid         (00:02:23)
[INFO]       AutoMut:  Mutating residue number 93 from chain A (valine) into aspartic acid         (00:02:24)
[INFO]       AutoMut:  Mutating residue number 93 from chain A (valine) into arginine              (00:02:30)
[INFO]       AutoMut:  Mutating residue number 93 from chain A (valine) into lysine                (00:02:31)
[INFO]       AutoMut:  Mutating residue number 82 from chain B (valine) into glutamic acid         (00:02:34)
[INFO]       AutoMut:  Mutating residue number 82 from chain B (valine) into lysine                (00:02:43)
[INFO]       AutoMut:  Mutating residue number 82 from chain B (valine) into aspartic acid         (00:02:44)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (tyrosine) into glutamic acid       (00:02:46)
[INFO]       AutoMut:  Mutating residue number 82 from chain B (valine) into arginine              (00:02:51)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (tyrosine) into lysine              (00:02:57)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (tyrosine) into aspartic acid       (00:03:03)
[INFO]       AutoMut:  Mutating residue number 60 from chain A (tyrosine) into arginine            (00:03:12)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain B (leucine) into glutamic    
                       acid: Energy difference: -0.0212 kcal/mol, Difference in average score from 
                       the base case: -0.0179                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain B (leucine) into lysine:     
                       Energy difference: 0.1020 kcal/mol, Difference in average score from the    
                       base case: -0.0164                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain B (leucine) into aspartic    
                       acid: Energy difference: -0.0389 kcal/mol, Difference in average score from 
                       the base case: -0.0175                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain B (leucine) into arginine:   
                       Energy difference: -0.0472 kcal/mol, Difference in average score from the   
                       base case: -0.0159                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain B (cysteine) into glutamic  
                       acid: Energy difference: -0.9486 kcal/mol, Difference in average score from 
                       the base case: -0.0159                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain B (cysteine) into lysine:   
                       Energy difference: -0.2734 kcal/mol, Difference in average score from the   
                       base case: -0.0154                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain B (cysteine) into aspartic  
                       acid: Energy difference: -0.6239 kcal/mol, Difference in average score from 
                       the base case: -0.0154                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain B (cysteine) into arginine: 
                       Energy difference: 0.0332 kcal/mol, Difference in average score from the    
                       base case: -0.0164                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 48 from chain B (tyrosine) into glutamic  
                       acid: Energy difference: 1.6985 kcal/mol, Difference in average score from  
                       the base case: -0.0072                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 48 from chain B (tyrosine) into lysine:   
                       Energy difference: 0.2558 kcal/mol, Difference in average score from the    
                       base case: -0.0062                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 48 from chain B (tyrosine) into aspartic  
                       acid: Energy difference: 3.2599 kcal/mol, Difference in average score from  
                       the base case: -0.0063                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 48 from chain B (tyrosine) into arginine: 
                       Energy difference: 0.4931 kcal/mol, Difference in average score from the    
                       base case: -0.0034                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain A (valine) into glutamic    
                       acid: Energy difference: 0.9131 kcal/mol, Difference in average score from  
                       the base case: -0.0075                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain A (valine) into lysine:     
                       Energy difference: -0.0612 kcal/mol, Difference in average score from the   
                       base case: -0.0062                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain A (valine) into aspartic    
                       acid: Energy difference: 0.3886 kcal/mol, Difference in average score from  
                       the base case: -0.0058                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 93 from chain A (valine) into arginine:   
                       Energy difference: -0.4679 kcal/mol, Difference in average score from the   
                       base case: -0.0045                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 82 from chain B (valine) into glutamic    
                       acid: Energy difference: 0.8372 kcal/mol, Difference in average score from  
                       the base case: -0.0040                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 82 from chain B (valine) into lysine:     
                       Energy difference: 0.5527 kcal/mol, Difference in average score from the    
                       base case: -0.0093                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 82 from chain B (valine) into aspartic    
                       acid: Energy difference: 1.9487 kcal/mol, Difference in average score from  
                       the base case: -0.0032                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 82 from chain B (valine) into arginine:   
                       Energy difference: 0.0030 kcal/mol, Difference in average score from the    
                       base case: -0.0079                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 3.4000 kcal/mol, Difference in average score from  
                       the base case: -0.0030                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (tyrosine) into lysine:   
                       Energy difference: 2.2290 kcal/mol, Difference in average score from the    
                       base case: -0.0030                                                          (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 4.0068 kcal/mol, Difference in average score from  
                       the base case: -0.0028                                                      (00:03:33)
[INFO]       AutoMut:  Effect of mutation residue number 60 from chain A (tyrosine) into arginine: 
                       Energy difference: 2.5711 kcal/mol, Difference in average score from the    
                       base case: -0.0044                                                          (00:03:33)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:39)
Show buried residues
Minimal score value
-2.1569
Maximal score value
1.172
Average score
-0.3592
Total score value
-83.3436
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 A -1.7444
2 V A -0.1987
3 Q A -1.1226
4 L A 0.0000
5 A A 0.0372
6 E A 0.0000
7 S A -0.2686
8 G A -0.3832
9 G A -0.2830
10 G A -0.2406
11 S A -0.3419
12 E A -0.7830
13 Q A -1.3249
14 P A -0.5791
15 G A -0.5231
16 G A -0.1807
17 S A -0.2351
18 L A -0.1390
19 R A -1.8876
20 L A 0.0000
21 S A -0.0341
22 C A 0.0000
23 A A 0.0326
24 G A 0.0000
25 S A -0.2969
26 G A -0.3933
27 F A 0.1910
28 T A -0.0195
29 F A 0.0000
30 S A -0.1718
31 S A -0.2807
32 Q A -0.3172
33 G A -0.1337
34 F A 0.0000
35 G A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.1403
40 A A -0.0610
41 P A -0.3373
42 G A -0.8114
43 K A -1.8062
44 G A -0.4445
45 L A 0.0000
46 E A -0.8505
47 W A 0.0000
48 V A 0.0000
49 S A 0.0000
50 S A -0.0308
51 I A 0.0000
52 S A -0.1113
53 A A -0.3653
54 D A -1.8139
55 G A -0.5144
56 S A -0.2876
57 G A -0.3156
58 T A -0.0681
59 Y A 0.2238
60 Y A 0.2366
61 A A 0.0000
62 D A -1.8060
63 S A -0.4127
64 V A 0.0000
65 K A -1.7849
66 G A -0.8203
67 R A -0.3333
68 F A 0.0000
69 T A -0.0529
70 I A 0.0000
71 S A -0.1425
72 R A -0.3210
73 D A -0.5870
74 N A -0.7543
75 S A -0.6228
76 K A -1.8299
77 N A -0.8800
78 T A -0.0944
79 L A 0.0000
80 Y A 0.1280
81 L A 0.0000
82 Q A -0.8760
83 M A 0.0000
84 N A -1.2995
85 S A -0.3822
86 L A 0.0000
87 R A -1.0905
88 A A -0.4641
89 E A -1.8094
90 D A 0.0000
91 T A -0.0156
92 A A 0.0000
93 V A 0.4899
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A -0.2114
99 L A 0.1278
100 S A -0.3773
101 R A -1.8234
102 V A 0.0000
103 R A -1.9468
104 V A 0.2002
105 G A -0.3910
106 S A -0.2984
107 T A -0.3852
108 R A -2.0623
109 G A 0.0000
110 V A 0.0775
111 V A 0.0000
112 G A 0.0000
113 D A -0.5507
114 V A 0.1436
115 W A 0.0000
116 G A 0.0000
117 Q A -1.2093
118 G A -0.2785
119 T A -0.0314
120 T A -0.0023
121 V A 0.0000
122 T A -0.0540
123 V A 0.0000
124 S A -0.2519
125 S A -0.2519
1 D B -1.7482
2 I B -0.0883
3 A B 0.0958
4 M B 0.0000
5 T B -0.0508
6 Q B 0.0000
7 S B -0.1629
8 P B 0.0721
9 L B 1.1720
10 S B -0.0678
11 L B 0.1278
12 P B -0.2796
13 V B 0.0000
14 T B -0.0775
15 P B -0.1960
16 G B -0.6632
17 E B -1.8842
18 P B -0.8151
19 A B 0.0000
20 S B -0.3204
21 I B 0.0000
22 S B -0.1096
23 C B 0.0000
24 R B -1.9969
25 S B 0.0000
26 S B -0.3832
27 Q B -1.5621
28 E B -2.0605
29 T B 0.0000
30 S B -0.0709
31 A B 0.0000
32 I B 0.0000
33 G B 0.0000
34 W B 0.0000
35 Y B 0.0000
36 L B 0.0000
37 Q B -0.2496
38 K B -0.7940
39 P B -0.4692
40 G B -0.7270
41 Q B -1.2862
42 S B -0.2435
43 P B 0.0000
44 Q B -1.0807
45 L B -0.0201
46 L B 0.0000
47 I B 0.0000
48 Y B 0.5096
49 G B 0.0000
50 T B 0.0000
51 S B -0.2266
52 T B -0.2871
53 R B -1.1652
54 G B -0.3057
55 S B -0.3074
56 G B -0.4742
57 V B 0.0685
58 P B -0.4019
59 D B -1.8732
60 R B -0.6978
61 F B 0.0000
62 S B -0.1768
63 G B -0.1467
64 S B -0.2744
65 G B -0.3682
66 S B -0.2951
67 G B -0.4199
68 T B -0.4729
69 D B -1.5626
70 F B 0.0000
71 T B -0.0298
72 L B 0.0000
73 K B -1.6704
74 I B 0.0000
75 S B -0.6145
76 R B -1.9229
77 V B 0.0000
78 E B -1.3003
79 A B -0.5079
80 E B -1.8097
81 D B 0.0000
82 V B 0.4297
83 G B 0.0000
84 V B 0.1583
85 Y B 0.0000
86 Y B 0.0000
87 C B 0.0000
88 M B 0.0000
89 Q B 0.0000
90 G B -0.0385
91 T B -0.0382
92 G B 0.0423
93 C B 0.7004
94 P B 0.1334
95 G B -0.0876
96 T B 0.0124
97 F B 0.1891
98 G B 0.0000
99 Q B -1.1983
100 G B 0.0000
101 T B 0.0000
102 K B -1.0025
103 L B 0.0000
104 E B -1.1065
105 I B -0.2581
106 K B -1.9919
107 R B -2.1569
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
CE93B -0.9486 -0.0159 View CSV PDB
CD93B -0.6239 -0.0154 View CSV PDB
LD9B -0.0389 -0.0175 View CSV PDB
LE9B -0.0212 -0.0179 View CSV PDB
VR93A -0.4679 -0.0045 View CSV PDB
VK93A -0.0612 -0.0062 View CSV PDB
VR82B 0.003 -0.0079 View CSV PDB
YK48B 0.2558 -0.0062 View CSV PDB
VK82B 0.5527 -0.0093 View CSV PDB
YR48B 0.4931 -0.0034 View CSV PDB
YR60A 2.5711 -0.0044 View CSV PDB
YK60A 2.229 -0.003 View CSV PDB