Project name: sericin1001

Status: done

Started: 2026-02-24 17:08:14
Chain sequence(s) A: MASMTGGQQMGRGSEFELGTSRMHLDSVSSTGSTSNTDSSSKSAGSRTSGGSSTYGYSSSHRGGSVSSTGSSSNTDSSTKNAGSSTSGGSSTYGYSSSHRGGSVSSTGSSSNTDSSTKSAGSSTSGGSSTYGYSSRHRGGRVSSTGSSSTTDASSNSVGSSTSGGSSTYGYSSNSRDGSSIGSRARRLQRPACKLAAALEHHHHHH
input PDB
Selected Chain(s) A
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 A 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                                          (00:01:28)
[INFO]       AutoMutEv:Residue number 1 from chain A and a score of 1.144 (methionine) selected    
                       for automated mutation                                                      (00:01:29)
[INFO]       AutoMutEv:Residue number 171 from chain A and a score of 0.999 (tyrosine) selected    
                       for automated mutation                                                      (00:01:29)
[INFO]       AutoMutEv:Residue number 195 from chain A and a score of 0.983 (leucine) selected for 
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Residue number 169 from chain A and a score of 0.976 (tyrosine) selected    
                       for automated mutation                                                      (00:01:29)
[INFO]       AutoMutEv:Residue number 181 from chain A and a score of 0.959 (isoleucine) selected  
                       for automated mutation                                                      (00:01:29)
[INFO]       AutoMutEv:Residue number 170 from chain A and a score of 0.867 (glycine) selected for 
                       automated mutation                                                          (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 1 from chain A (methionine) into arginine           (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 171 from chain A (tyrosine) into histidine          (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 171 from chain A (tyrosine) into tryptophan         (00:01:29)
[INFO]       AutoMutEv:Mutating residue number 195 from chain A (leucine) into methionine          (00:01:34)
[INFO]       AutoMutEv:Mutating residue number 1 from chain A (methionine) into lysine             (00:01:35)
[INFO]       AutoMutEv:Mutating residue number 171 from chain A (tyrosine) into cysteine           (00:01:36)
[INFO]       AutoMutEv:Mutating residue number 169 from chain A (tyrosine) into histidine          (00:01:40)
[INFO]       AutoMutEv:Mutating residue number 169 from chain A (tyrosine) into tryptophan         (00:01:41)
[INFO]       AutoMutEv:Mutating residue number 181 from chain A (isoleucine) into methionine       (00:01:42)
[INFO]       AutoMutEv:Mutating residue number 181 from chain A (isoleucine) into threonine        (00:01:48)
[INFO]       AutoMutEv:Mutating residue number 181 from chain A (isoleucine) into leucine          (00:01:48)
[INFO]       AutoMutEv:Mutating residue number 169 from chain A (tyrosine) into cysteine           (00:01:50)
[INFO]       AutoMutEv:Mutating residue number 170 from chain A (glycine) into glutamic acid       (00:01:57)
[INFO]       AutoMutEv:Mutating residue number 170 from chain A (glycine) into asparagine          (00:01:58)
[INFO]       AutoMutEv:Mutating residue number 170 from chain A (glycine) into aspartic acid       (00:02:03)
[INFO]       AutoMutEv:Effect of mutation residue number 1 from chain A (methionine) into          
                       arginine: Energy difference: -0.1862 kcal/mol, Difference in average score  
                       from the base case: -0.0259                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 1 from chain A (methionine) into lysine:  
                       Energy difference: -0.2177 kcal/mol, Difference in average score from the   
                       base case: -0.0246                                                          (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 171 from chain A (tyrosine) into          
                       histidine: Energy difference: 0.3641 kcal/mol, Difference in average score  
                       from the base case: -0.0343                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 171 from chain A (tyrosine) into          
                       cysteine: Energy difference: 0.5015 kcal/mol, Difference in average score   
                       from the base case: -0.0184                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 171 from chain A (tyrosine) into          
                       tryptophan: Energy difference: 0.1396 kcal/mol, Difference in average score 
                       from the base case: -0.0005                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 195 from chain A (leucine) into           
                       methionine: Energy difference: 0.3458 kcal/mol, Difference in average score 
                       from the base case: -0.0066                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 169 from chain A (tyrosine) into          
                       histidine: Energy difference: 0.4166 kcal/mol, Difference in average score  
                       from the base case: -0.0420                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 169 from chain A (tyrosine) into          
                       cysteine: Energy difference: 0.3626 kcal/mol, Difference in average score   
                       from the base case: -0.0097                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 169 from chain A (tyrosine) into          
                       tryptophan: Energy difference: -0.2122 kcal/mol, Difference in average      
                       score from the base case: -0.0030                                           (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 181 from chain A (isoleucine) into        
                       threonine: Energy difference: 0.4435 kcal/mol, Difference in average score  
                       from the base case: -0.0351                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 181 from chain A (isoleucine) into        
                       methionine: Energy difference: 0.1704 kcal/mol, Difference in average score 
                       from the base case: -0.0157                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 181 from chain A (isoleucine) into        
                       leucine: Energy difference: 0.0183 kcal/mol, Difference in average score    
                       from the base case: -0.0066                                                 (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 170 from chain A (glycine) into glutamic  
                       acid: Energy difference: 0.0769 kcal/mol, Difference in average score from  
                       the base case: -0.0039                                                      (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 170 from chain A (glycine) into aspartic  
                       acid: Energy difference: -0.0467 kcal/mol, Difference in average score from 
                       the base case: -0.0035                                                      (00:02:09)
[INFO]       AutoMutEv:Effect of mutation residue number 170 from chain A (glycine) into           
                       asparagine: Energy difference: -0.3934 kcal/mol, Difference in average      
                       score from the base case: 0.0004                                            (00:02:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:14)
Show buried residues
Minimal score value
-3.8129
Maximal score value
1.1444
Average score
-0.7531
Total score value
-155.1389
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 M A 1.1444
2 A A 0.7089
3 S A 0.5167
4 M A 0.8624
5 T A -0.1143
6 G A -0.9142
7 G A -1.3873
8 Q A -1.9162
9 Q A -1.7797
10 M A -0.6201
11 G A -1.5201
12 R A -2.4358
13 G A -1.7668
14 S A -1.8129
15 E A -2.3447
16 F A -1.0049
17 E A -2.1785
18 L A -1.0806
19 G A -1.3321
20 T A -1.1412
21 S A -1.3605
22 R A -1.8434
23 M A -0.4779
24 H A -0.6531
25 L A 0.7434
26 D A -0.2461
27 S A -0.1132
28 V A -0.0709
29 S A -0.2549
30 S A 0.0000
31 T A -0.3306
32 G A -0.8990
33 S A -0.8192
34 T A -0.7032
35 S A 0.0000
36 N A -1.1920
37 T A 0.0000
38 D A -1.9784
39 S A 0.0000
40 S A -1.4849
41 S A -1.7246
42 K A -2.9810
43 S A -1.7030
44 A A -1.1450
45 G A -0.5944
46 S A -0.1586
47 R A 0.0000
48 T A -0.2312
49 S A 0.0000
50 G A -0.4180
51 G A -0.5224
52 S A -0.6090
53 S A -0.3857
54 T A 0.0000
55 Y A 0.2995
56 G A 0.0000
57 Y A -0.2791
58 S A 0.0000
59 S A -1.4637
60 S A 0.0000
61 H A -3.3583
62 R A -3.6307
63 G A 0.0000
64 G A -1.2627
65 S A -0.3218
66 V A 0.0000
67 S A -0.2484
68 S A 0.0000
69 T A -0.2824
70 G A -0.4392
71 S A -0.5776
72 S A -0.2138
73 S A 0.0000
74 N A 0.0000
75 T A 0.0000
76 D A -0.3410
77 S A 0.0000
78 S A -0.8381
79 T A 0.0000
80 K A -3.8129
81 N A -3.1221
82 A A -1.7301
83 G A -1.2923
84 S A -0.2782
85 S A 0.0000
86 T A -0.2004
87 S A 0.0000
88 G A -0.2974
89 G A -0.4389
90 S A -0.5415
91 S A -0.3353
92 T A 0.0000
93 Y A 0.5662
94 G A 0.0000
95 Y A 0.2389
96 S A 0.0000
97 S A -1.1203
98 S A 0.0000
99 H A -3.2049
100 R A -3.6076
101 G A 0.0000
102 G A 0.0000
103 S A -0.3861
104 V A 0.0000
105 S A -0.2039
106 S A 0.0000
107 T A -0.3147
108 G A -0.4504
109 S A -0.5398
110 S A -0.2916
111 S A 0.0000
112 N A 0.3033
113 T A 0.0000
114 D A -0.0758
115 S A 0.0000
116 S A -0.6357
117 T A 0.0000
118 K A -3.4451
119 S A -2.8237
120 A A -1.6233
121 G A -1.3678
122 S A -0.6817
123 S A 0.0000
124 T A -0.3436
125 S A 0.0000
126 G A -0.3001
127 G A -0.4365
128 S A -0.5576
129 S A -0.3489
130 T A 0.0000
131 Y A 0.8585
132 G A 0.0000
133 Y A 0.5083
134 S A 0.0000
135 S A -1.0134
136 R A 0.0000
137 H A -3.1478
138 R A -3.3337
139 G A 0.0000
140 G A -1.3753
141 R A -1.2487
142 V A 0.0000
143 S A -0.3114
144 S A 0.0000
145 T A -0.2702
146 G A -0.4428
147 S A -0.5857
148 S A -0.1962
149 S A 0.0000
150 T A 0.7903
151 T A 0.0000
152 D A 0.4705
153 A A 0.0000
154 S A -0.5590
155 S A -2.0739
156 N A -2.8188
157 S A -2.2741
158 V A -1.3752
159 G A -1.4279
160 S A -0.6211
161 S A 0.0000
162 T A 0.1175
163 S A 0.0000
164 G A -0.4985
165 G A -0.8047
166 S A -1.1159
167 S A -0.5515
168 T A -0.2559
169 Y A 0.9763
170 G A 0.8673
171 Y A 0.9990
172 S A 0.1983
173 S A -0.8067
174 N A -2.1141
175 S A -2.3026
176 R A -3.1429
177 D A -2.7467
178 G A -2.0810
179 S A -0.7986
180 S A 0.2199
181 I A 0.9592
182 G A -0.1280
183 S A -1.1889
184 R A -2.6040
185 A A -2.2862
186 R A -3.0383
187 R A -2.8439
188 L A -1.0330
189 Q A -2.2261
190 R A -2.2356
191 P A -1.2653
192 A A -0.6311
193 C A 0.0663
194 K A -0.5847
195 L A 0.9829
196 A A 0.6430
197 A A 0.5139
198 A A 0.4351
199 L A 0.3630
200 E A -1.8795
201 H A -2.3496
202 H A -2.4769
203 H A -2.6478
204 H A -2.5338
205 H A -2.2075
206 H A -1.7228
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
MR1A -0.1862 -0.0259 View CSV PDB
MK1A -0.2177 -0.0246 View CSV PDB
YW169A -0.2122 -0.003 View CSV PDB
GD170A -0.0467 -0.0035 View CSV PDB
IL181A 0.0183 -0.0066 View CSV PDB
YH169A 0.4166 -0.042 View CSV PDB
YH171A 0.3641 -0.0343 View CSV PDB
IM181A 0.1704 -0.0157 View CSV PDB
GE170A 0.0769 -0.0039 View CSV PDB
YC171A 0.5015 -0.0184 View CSV PDB
LM195A 0.3458 -0.0066 View CSV PDB