Project name: CmDLH

Status: done

Started: 2026-06-15 16:39:54
Chain sequence(s) A: MQCTESPSILPVNDGWLFSIVDRPNASGRFPAVVMLHGFTGNHIEANRLYVDIARALCGAGFVVVRFDYRNHGDSSGLFEDFDIENAVNDAEYMVNYTLKLGYVDSSRLALIGLSMGGHIALRIYSRMPNIVKAVILLSPGISFRGIGKLLEQARGDYVYFGAFRLRVSNVTKMANSDAMSVADLINVPVMIIHAKDDEAVPYQQSVEFHNRVKYNDKTLVLLDKGGHVFSDYEIKSKVIEAIVNWLREKLRVS
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
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 A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:38)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:38)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:07)
[INFO]       AutoMut:  Residue number 9 from chain A and a score of 1.706 (isoleucine) selected    
                       for automated mutation                                                      (00:05:09)
[INFO]       AutoMut:  Residue number 253 from chain A and a score of 1.545 (valine) selected for  
                       automated mutation                                                          (00:05:09)
[INFO]       AutoMut:  Residue number 78 from chain A and a score of 1.444 (leucine) selected for  
                       automated mutation                                                          (00:05:09)
[INFO]       AutoMut:  Residue number 185 from chain A and a score of 1.413 (leucine) selected for 
                       automated mutation                                                          (00:05:09)
[INFO]       AutoMut:  Residue number 233 from chain A and a score of 0.929 (tyrosine) selected    
                       for automated mutation                                                      (00:05:09)
[INFO]       AutoMut:  Residue number 164 from chain A and a score of 0.711 (phenylalanine)        
                       selected for automated mutation                                             (00:05:09)
[INFO]       AutoMut:  Mutating residue number 9 from chain A (isoleucine) into glutamic acid      (00:05:09)
[INFO]       AutoMut:  Mutating residue number 9 from chain A (isoleucine) into aspartic acid      (00:05:09)
[INFO]       AutoMut:  Mutating residue number 253 from chain A (valine) into glutamic acid        (00:05:09)
[INFO]       AutoMut:  Mutating residue number 9 from chain A (isoleucine) into arginine           (00:05:22)
[INFO]       AutoMut:  Mutating residue number 253 from chain A (valine) into lysine               (00:05:23)
[INFO]       AutoMut:  Mutating residue number 9 from chain A (isoleucine) into lysine             (00:05:25)
[INFO]       AutoMut:  Mutating residue number 253 from chain A (valine) into aspartic acid        (00:05:41)
[INFO]       AutoMut:  Mutating residue number 78 from chain A (leucine) into glutamic acid        (00:05:49)
[INFO]       AutoMut:  Mutating residue number 78 from chain A (leucine) into aspartic acid        (00:05:53)
[INFO]       AutoMut:  Mutating residue number 253 from chain A (valine) into arginine             (00:05:54)
[INFO]       AutoMut:  Mutating residue number 78 from chain A (leucine) into arginine             (00:06:04)
[INFO]       AutoMut:  Mutating residue number 78 from chain A (leucine) into lysine               (00:06:05)
[INFO]       AutoMut:  Mutating residue number 185 from chain A (leucine) into glutamic acid       (00:06:17)
[INFO]       AutoMut:  Mutating residue number 185 from chain A (leucine) into aspartic acid       (00:06:33)
[INFO]       AutoMut:  Mutating residue number 233 from chain A (tyrosine) into glutamic acid      (00:06:34)
[INFO]       AutoMut:  Mutating residue number 185 from chain A (leucine) into lysine              (00:06:39)
[INFO]       AutoMut:  Mutating residue number 185 from chain A (leucine) into arginine            (00:06:47)
[INFO]       AutoMut:  Mutating residue number 233 from chain A (tyrosine) into lysine             (00:06:55)
[INFO]       AutoMut:  Mutating residue number 233 from chain A (tyrosine) into aspartic acid      (00:07:12)
[INFO]       AutoMut:  Mutating residue number 164 from chain A (phenylalanine) into glutamic acid 
                       Mutating residue number 164 from chain A (phenylalanine) into glutamic acid (00:07:15)
[INFO]       AutoMut:  Mutating residue number 164 from chain A (phenylalanine) into aspartic acid 
                       Mutating residue number 164 from chain A (phenylalanine) into aspartic acid (00:07:23)
[INFO]       AutoMut:  Mutating residue number 164 from chain A (phenylalanine) into lysine        (00:07:26)
[INFO]       AutoMut:  Mutating residue number 233 from chain A (tyrosine) into arginine           (00:07:28)
[INFO]       AutoMut:  Mutating residue number 164 from chain A (phenylalanine) into arginine      (00:07:35)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain A (isoleucine) into glutamic 
                       acid: Energy difference: 0.9485 kcal/mol, Difference in average score from  
                       the base case: -0.0209                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain A (isoleucine) into lysine:  
                       Energy difference: 0.4117 kcal/mol, Difference in average score from the    
                       base case: -0.0208                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain A (isoleucine) into aspartic 
                       acid: Energy difference: 1.9930 kcal/mol, Difference in average score from  
                       the base case: -0.0189                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 9 from chain A (isoleucine) into          
                       arginine: Energy difference: -1.6312 kcal/mol, Difference in average score  
                       from the base case: -0.0220                                                 (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 253 from chain A (valine) into glutamic   
                       acid: Energy difference: -0.0653 kcal/mol, Difference in average score from 
                       the base case: -0.0198                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 253 from chain A (valine) into lysine:    
                       Energy difference: -0.8980 kcal/mol, Difference in average score from the   
                       base case: -0.0183                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 253 from chain A (valine) into aspartic   
                       acid: Energy difference: -0.0124 kcal/mol, Difference in average score from 
                       the base case: -0.0198                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 253 from chain A (valine) into arginine:  
                       Energy difference: -1.2100 kcal/mol, Difference in average score from the   
                       base case: -0.0198                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 78 from chain A (leucine) into glutamic   
                       acid: Energy difference: -0.2386 kcal/mol, Difference in average score from 
                       the base case: -0.0195                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 78 from chain A (leucine) into lysine:    
                       Energy difference: -0.1879 kcal/mol, Difference in average score from the   
                       base case: -0.0170                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 78 from chain A (leucine) into aspartic   
                       acid: Energy difference: 0.1712 kcal/mol, Difference in average score from  
                       the base case: -0.0196                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 78 from chain A (leucine) into arginine:  
                       Energy difference: -0.7134 kcal/mol, Difference in average score from the   
                       base case: -0.0139                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 185 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.8618 kcal/mol, Difference in average score from  
                       the base case: -0.0158                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 185 from chain A (leucine) into lysine:   
                       Energy difference: -0.0817 kcal/mol, Difference in average score from the   
                       base case: -0.0137                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 185 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.0592 kcal/mol, Difference in average score from  
                       the base case: -0.0161                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 185 from chain A (leucine) into arginine: 
                       Energy difference: -0.2823 kcal/mol, Difference in average score from the   
                       base case: -0.0153                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 233 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: -0.5782 kcal/mol, Difference in average score from 
                       the base case: -0.0175                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 233 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.3933 kcal/mol, Difference in average score from the   
                       base case: -0.0172                                                          (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 233 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.0489 kcal/mol, Difference in average score from  
                       the base case: -0.0175                                                      (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 233 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.6951 kcal/mol, Difference in average score  
                       from the base case: -0.0188                                                 (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 164 from chain A (phenylalanine) into     
                       glutamic acid: Energy difference: 2.9211 kcal/mol, Difference in average    
                       score from the base case: -0.0057                                           (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 164 from chain A (phenylalanine) into     
                       lysine: Energy difference: 1.9698 kcal/mol, Difference in average score     
                       from the base case: -0.0093                                                 (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 164 from chain A (phenylalanine) into     
                       aspartic acid: Energy difference: 3.4255 kcal/mol, Difference in average    
                       score from the base case: -0.0048                                           (00:08:15)
[INFO]       AutoMut:  Effect of mutation residue number 164 from chain A (phenylalanine) into     
                       arginine: Energy difference: 1.7527 kcal/mol, Difference in average score   
                       from the base case: -0.0091                                                 (00:08:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:25)
Show buried residues
Minimal score value
-2.0703
Maximal score value
1.7065
Average score
-0.2995
Total score value
-75.761
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
2 Q A -1.1624
3 C A -0.0203
4 T A -0.3241
5 E A -1.7267
6 S A -0.5475
7 P A -0.2994
8 S A 0.2132
9 I A 1.7065
10 L A 0.4294
11 P A -0.0864
12 V A -0.0570
13 N A -1.5557
14 D A -2.0369
15 G A -0.2874
16 W A 0.6729
17 L A 0.0000
18 F A 0.4141
19 S A 0.0000
20 I A 0.0000
21 V A 0.0000
22 D A 0.0000
23 R A -0.5985
24 P A 0.0000
25 N A -1.2650
26 A A -0.2321
27 S A -0.2717
28 G A -0.7571
29 R A -1.8770
30 F A -0.1007
31 P A 0.0000
32 A A 0.0000
33 V A 0.0000
34 V A 0.0000
35 M A 0.0000
36 L A 0.0000
37 H A 0.0000
38 G A 0.0000
39 F A 0.3073
40 T A 0.0084
41 G A -0.1437
42 N A -0.3510
43 H A 0.0000
44 I A 0.4579
45 E A -0.0853
46 A A -0.2399
47 N A -1.5959
48 R A -2.0703
49 L A 0.0000
50 Y A 0.0000
51 V A 0.0431
52 D A -0.9363
53 I A 0.0000
54 A A 0.0000
55 R A -1.3813
56 A A -0.2379
57 L A 0.0000
58 C A 0.0000
59 G A -0.4649
60 A A -0.0945
61 G A -0.0744
62 F A 0.0000
63 V A 0.0000
64 V A 0.0000
65 V A 0.0000
66 R A 0.0000
67 F A 0.0000
68 D A 0.0000
69 Y A 0.0000
70 R A -0.2128
71 N A -0.0633
72 H A 0.0000
73 G A -0.8059
74 D A -1.8779
75 S A 0.0000
76 S A -0.1023
77 G A -0.1961
78 L A 1.4437
79 F A 0.0000
80 E A 0.0000
81 D A -1.4680
82 F A 0.0000
83 D A -0.1885
84 I A 0.0000
85 E A -0.8334
86 N A -0.6147
87 A A 0.0000
88 V A 0.0000
89 N A -0.7061
90 D A 0.0000
91 A A 0.0000
92 E A -0.4955
93 Y A 0.3191
94 M A 0.0000
95 V A 0.0000
96 N A -0.3681
97 Y A 0.1094
98 T A 0.0000
99 L A -0.0857
100 K A -1.6230
101 L A -0.1984
102 G A -0.3964
103 Y A -0.1424
104 V A 0.0000
105 D A -0.5318
106 S A -0.1840
107 S A -0.2909
108 R A -0.3833
109 L A 0.0000
110 A A 0.0000
111 L A 0.0000
112 I A 0.0000
113 G A 0.0000
114 L A 0.0000
115 S A -0.0218
116 M A 0.0000
117 G A 0.0000
118 G A 0.0000
119 H A 0.0000
120 I A 0.0000
121 A A 0.0000
122 L A 0.0000
123 R A -0.2748
124 I A 0.0000
125 Y A 0.0000
126 S A -0.3538
127 R A -1.4352
128 M A -0.1947
129 P A -0.4440
130 N A -1.2352
131 I A 0.1902
132 V A 0.0000
133 K A -0.5812
134 A A 0.0000
135 V A 0.0000
136 I A 0.0000
137 L A 0.0000
138 L A 0.0000
139 S A 0.0000
140 P A 0.0000
141 G A 0.0000
142 I A 0.0000
143 S A 0.0000
144 F A 0.0000
145 R A -1.9014
146 G A -0.6048
147 I A 0.1932
148 G A -0.3698
149 K A -1.6280
150 L A 0.2674
151 L A 0.1780
152 E A -1.9697
153 Q A -1.5348
154 A A -0.5457
155 R A -1.9248
156 G A -1.1265
157 D A -1.8387
158 Y A -0.2281
159 V A 0.0000
160 Y A 0.5314
161 F A 0.4064
162 G A -0.4022
163 A A 0.1249
164 F A 0.7113
165 R A -0.5654
166 L A 0.0000
167 R A -0.5104
168 V A 0.2623
169 S A -0.1604
170 N A -0.2671
171 V A 0.0000
172 T A -0.2136
173 K A -0.9925
174 M A 0.0000
175 A A -0.4776
176 N A -1.2717
177 S A 0.0000
178 D A -0.9829
179 A A 0.0000
180 M A 0.0000
181 S A -0.2010
182 V A 0.0000
183 A A 0.0000
184 D A -0.4386
185 L A 1.4125
186 I A 0.0000
187 N A -1.2730
188 V A 0.0000
189 P A -0.0813
190 V A 0.0000
191 M A 0.0000
192 I A 0.0000
193 I A 0.0000
194 H A 0.0000
195 A A 0.0000
196 K A -1.6871
197 D A -1.8773
198 D A 0.0000
199 E A -1.8090
200 A A -0.2814
201 V A 0.0000
202 P A -0.1533
203 Y A 0.0078
204 Q A -1.1332
205 Q A -0.3911
206 S A 0.0000
207 V A 0.0177
208 E A -1.7313
209 F A 0.0000
210 H A -0.3304
211 N A -1.4515
212 R A -1.1082
213 V A 0.0000
214 K A -1.6409
215 Y A -0.2273
216 N A -1.3052
217 D A -0.8085
218 K A -0.6341
219 T A -0.0504
220 L A 0.4448
221 V A 0.4775
222 L A 0.6050
223 L A 0.0000
224 D A -2.0282
225 K A -1.6572
226 G A 0.0000
227 G A -0.1305
228 H A -0.1348
229 V A 0.2665
230 F A 0.0000
231 S A -0.2706
232 D A -0.1152
233 Y A 0.9292
234 E A -1.5405
235 I A -0.1806
236 K A -0.2730
237 S A -0.3645
238 K A -1.0079
239 V A 0.0000
240 I A 0.0000
241 E A -1.8177
242 A A -0.3232
243 I A 0.0000
244 V A 0.0830
245 N A -0.5837
246 W A 0.0000
247 L A 0.0000
248 R A -1.2617
249 E A -2.0624
250 K A -0.8241
251 L A 0.0000
252 R A -0.7504
253 V A 1.5447
254 S A 0.1071
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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
IR9A -1.6312 -0.022 View CSV PDB
VR253A -1.21 -0.0198 View CSV PDB
VK253A -0.898 -0.0183 View CSV PDB
YR233A -0.6951 -0.0188 View CSV PDB
YE233A -0.5782 -0.0175 View CSV PDB
LR78A -0.7134 -0.0139 View CSV PDB
LE78A -0.2386 -0.0195 View CSV PDB
LR185A -0.2823 -0.0153 View CSV PDB
LK185A -0.0817 -0.0137 View CSV PDB
IK9A 0.4117 -0.0208 View CSV PDB
FR164A 1.7527 -0.0091 View CSV PDB
FK164A 1.9698 -0.0093 View CSV PDB