Project name: lilly

Status: done

Started: 2026-06-23 02:07:01
Settings
Chain sequence(s) A: EVQLVESGGGLVKPGGSLRLSCVASGFTFSSYSMNWVRQAPGKGLEWVSSISSSSSYIYYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTAVYYCARRHGYSNSDAFDNWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH
B: DIQMTQSPSAMSASVGDRVTITCRASQGISHYLVWFQQKPGKVPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNSYPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
input PDB
Selected Chain(s) A,B
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode No
Automated mutations Yes
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[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 minimalization                                        (00:00:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:04:32)
[INFO]       Auto_mut: Residue number 58 from chain A and a score of 1.847 (isoleucine) selected   
                       for automated muatation                                                     (00:04:35)
[INFO]       Auto_mut: Residue number 57 from chain A and a score of 1.736 (tyrosine) selected for 
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 59 from chain A and a score of 1.216 (tyrosine) selected for 
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 178 from chain A and a score of 1.196 (leucine) selected for 
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 5 from chain A and a score of 0.840 (valine) selected for    
                       automated muatation                                                         (00:04:35)
[INFO]       Auto_mut: Residue number 102 from chain A and a score of 0.809 (tyrosine) selected    
                       for automated muatation                                                     (00:04:35)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (isoleucine) into glutamic acid     (00:04:35)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (isoleucine) into aspartic acid     (00:04:35)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (tyrosine) into glutamic acid       (00:04:35)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (isoleucine) into lysine            (00:06:37)
[INFO]       Auto_mut: Mutating residue number 58 from chain A (isoleucine) into arginine          (00:06:39)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (tyrosine) into lysine              (00:06:40)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (tyrosine) into aspartic acid       (00:08:45)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into glutamic acid       (00:08:46)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into aspartic acid       (00:08:47)
[INFO]       Auto_mut: Mutating residue number 57 from chain A (tyrosine) into arginine            (00:10:54)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into lysine              (00:10:57)
[INFO]       Auto_mut: Mutating residue number 59 from chain A (tyrosine) into arginine            (00:11:00)
[INFO]       Auto_mut: Mutating residue number 178 from chain A (leucine) into glutamic acid       (00:13:02)
[INFO]       Auto_mut: Mutating residue number 178 from chain A (leucine) into aspartic acid       (00:13:06)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into glutamic acid          (00:13:12)
[INFO]       Auto_mut: Mutating residue number 178 from chain A (leucine) into lysine              (00:15:02)
[INFO]       Auto_mut: Mutating residue number 178 from chain A (leucine) into arginine            (00:15:07)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into lysine                 (00:15:25)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into aspartic acid          (00:17:08)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (tyrosine) into glutamic acid      (00:17:09)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (tyrosine) into aspartic acid      (00:17:48)
[INFO]       Auto_mut: Mutating residue number 5 from chain A (valine) into arginine               (00:19:10)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (tyrosine) into lysine             (00:19:13)
[INFO]       Auto_mut: Mutating residue number 102 from chain A (tyrosine) into arginine           (00:19:47)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (isoleucine) into         
                       glutamic acid: Energy difference: 1.1221 kcal/mol, Difference in average    
                       score from the base case: -0.0190                                           (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (isoleucine) into lysine: 
                       Energy difference: 0.5656 kcal/mol, Difference in average score from the    
                       base case: -0.0150                                                          (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (isoleucine) into         
                       aspartic acid: Energy difference: 1.4006 kcal/mol, Difference in average    
                       score from the base case: -0.0183                                           (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 58 from chain A (isoleucine) into         
                       arginine: Energy difference: 0.0950 kcal/mol, Difference in average score   
                       from the base case: -0.0104                                                 (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: -1.2557 kcal/mol, Difference in average score from 
                       the base case: -0.0176                                                      (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (tyrosine) into lysine:   
                       Energy difference: -0.8575 kcal/mol, Difference in average score from the   
                       base case: -0.0183                                                          (00:21:50)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: -1.3911 kcal/mol, Difference in average score from 
                       the base case: -0.0131                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 57 from chain A (tyrosine) into arginine: 
                       Energy difference: -0.7998 kcal/mol, Difference in average score from the   
                       base case: -0.0224                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into glutamic  
                       acid: Energy difference: 2.5543 kcal/mol, Difference in average score from  
                       the base case: -0.0068                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into lysine:   
                       Energy difference: 1.3139 kcal/mol, Difference in average score from the    
                       base case: -0.0095                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into aspartic  
                       acid: Energy difference: 2.5889 kcal/mol, Difference in average score from  
                       the base case: -0.0043                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 59 from chain A (tyrosine) into arginine: 
                       Energy difference: 1.9791 kcal/mol, Difference in average score from the    
                       base case: -0.0109                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain A (leucine) into glutamic  
                       acid: Energy difference: 0.8796 kcal/mol, Difference in average score from  
                       the base case: -0.0273                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain A (leucine) into lysine:   
                       Energy difference: -0.0071 kcal/mol, Difference in average score from the   
                       base case: -0.0229                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain A (leucine) into aspartic  
                       acid: Energy difference: 1.4675 kcal/mol, Difference in average score from  
                       the base case: -0.0264                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 178 from chain A (leucine) into arginine: 
                       Energy difference: 0.0761 kcal/mol, Difference in average score from the    
                       base case: -0.0269                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into glutamic     
                       acid: Energy difference: 0.1099 kcal/mol, Difference in average score from  
                       the base case: -0.0166                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into lysine:      
                       Energy difference: -0.7363 kcal/mol, Difference in average score from the   
                       base case: -0.0144                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into aspartic     
                       acid: Energy difference: 0.9396 kcal/mol, Difference in average score from  
                       the base case: -0.0106                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 5 from chain A (valine) into arginine:    
                       Energy difference: -0.7013 kcal/mol, Difference in average score from the   
                       base case: -0.0182                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (tyrosine) into glutamic 
                       acid: Energy difference: 0.2723 kcal/mol, Difference in average score from  
                       the base case: -0.0204                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (tyrosine) into lysine:  
                       Energy difference: -0.2598 kcal/mol, Difference in average score from the   
                       base case: -0.0175                                                          (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (tyrosine) into aspartic 
                       acid: Energy difference: 0.2355 kcal/mol, Difference in average score from  
                       the base case: -0.0193                                                      (00:21:51)
[INFO]       Auto_mut: Effect of mutation residue number 102 from chain A (tyrosine) into          
                       arginine: Energy difference: -0.1069 kcal/mol, Difference in average score  
                       from the base case: -0.0146                                                 (00:21:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:59)
Show buried residues
Minimal score value
-3.4651
Maximal score value
1.8472
Average score
-0.692
Total score value
-305.8717
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 E A -2.1780
2 V A -1.5080
3 Q A -1.4325
4 L A 0.0000
5 V A 0.8404
6 E A 0.0000
7 S A -0.3578
8 G A -0.8975
9 G A -0.4762
10 G A -0.4358
11 L A -0.1190
12 V A -0.8271
13 K A -2.0622
14 P A -1.9153
15 G A -1.5549
16 G A -1.2759
17 S A -1.3768
18 L A -1.2132
19 R A -2.1306
20 L A 0.0000
21 S A -0.2333
22 C A 0.0000
23 V A 0.6846
24 A A 0.0000
25 S A -0.9048
26 G A -1.3309
27 F A -0.5911
28 T A -0.2411
29 F A 0.0000
30 S A -0.7326
31 S A -0.0455
32 Y A 0.0000
33 S A 0.0000
34 M A 0.0000
35 N A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.7432
40 A A -1.1580
41 P A -0.9968
42 G A -1.5070
43 K A -2.3602
44 G A -1.6140
45 L A 0.0000
46 E A -1.0007
47 W A 0.0000
48 V A 0.0000
49 S A 0.0000
50 S A 0.0000
51 I A 0.0000
52 S A 0.3932
53 S A -0.2707
54 S A -0.2258
55 S A 0.0765
56 S A 0.4958
57 Y A 1.7363
58 I A 1.8472
59 Y A 1.2155
60 Y A -0.2484
61 A A 0.0000
62 D A -2.5646
63 S A -1.7489
64 V A 0.0000
65 K A -2.4277
66 G A -1.7013
67 R A -1.4512
68 F A 0.0000
69 T A -0.6265
70 I A 0.0000
71 S A -0.2378
72 R A -0.8194
73 D A -1.3128
74 N A -1.5334
75 A A -1.2946
76 K A -2.0619
77 N A -1.3512
78 S A 0.0000
79 L A 0.0000
80 Y A -0.4187
81 L A 0.0000
82 Q A -1.2509
83 M A 0.0000
84 N A -1.5047
85 S A -1.3473
86 L A 0.0000
87 R A -2.3450
88 A A -1.7437
89 E A -2.2170
90 D A 0.0000
91 T A -0.6880
92 A A 0.0000
93 V A 0.3455
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A 0.0000
99 R A -0.8582
100 H A -0.8245
101 G A -0.0958
102 Y A 0.8095
103 S A -0.3433
104 N A -1.2749
105 S A -0.7982
106 D A -0.9043
107 A A 0.0000
108 F A 0.0000
109 D A -1.0659
110 N A -0.8980
111 W A 0.0000
112 G A 0.0000
113 Q A -1.2441
114 G A -0.3898
115 T A -0.0605
116 L A 0.2278
117 V A 0.0000
118 T A 0.0000
119 V A 0.0000
120 S A -1.1097
121 S A -0.8758
122 A A -0.5303
123 S A -0.6276
124 T A -0.5873
125 K A -1.1643
126 G A -1.3549
127 P A 0.0000
128 S A -0.4334
129 V A 0.0000
130 F A 0.0000
131 P A -1.2510
132 L A 0.0000
133 A A -1.3099
134 P A 0.0000
135 S A -0.9917
136 S A -0.7836
137 K A -1.0709
138 S A 0.0000
139 T A -0.6990
140 S A -0.6909
141 G A -0.7905
142 G A -0.8599
143 T A -0.5999
144 A A 0.0000
145 A A 0.0000
146 L A 0.0000
147 G A 0.0000
148 C A 0.0000
149 L A 0.0000
150 V A 0.0000
151 K A 0.0000
152 D A -0.3565
153 Y A 0.0000
154 F A 0.0000
155 P A 0.0000
156 E A -0.4395
157 P A -0.7376
158 V A -0.7682
159 T A -0.7017
160 V A -0.2174
161 S A -0.3984
162 W A 0.0000
163 N A -0.6710
164 S A -0.6143
165 G A -0.4777
166 A A -0.2239
167 L A 0.0405
168 T A -0.1532
169 S A -0.1639
170 G A -0.1924
171 V A 0.1943
172 H A -0.2908
173 T A 0.0271
174 F A 0.0000
175 P A -0.2849
176 A A 0.2525
177 V A 0.5644
178 L A 1.1959
179 Q A 0.3104
180 S A -0.0479
181 S A -0.1871
182 G A 0.0622
183 L A 0.1592
184 Y A 0.4775
185 S A 0.0000
186 L A 0.0000
187 S A 0.0000
188 S A 0.0000
189 V A 0.0000
190 V A 0.0000
191 T A -0.1233
192 V A 0.0000
193 P A -0.5991
194 S A -0.5623
195 S A -0.5670
196 S A -0.5388
197 L A -0.7400
198 G A -0.9251
199 T A -0.6538
200 Q A -1.0829
201 T A -0.9962
202 Y A 0.0000
203 I A -1.0280
204 C A 0.0000
205 N A -1.4430
206 V A 0.0000
207 N A -2.3184
208 H A 0.0000
209 K A -2.8361
210 P A -1.6029
211 S A -1.8627
212 N A -2.6347
213 T A -2.1673
214 K A -2.8277
215 V A -1.5760
216 D A -2.3024
217 K A -1.8944
218 K A -2.2215
219 V A 0.0000
220 E A -2.7979
221 P A -1.8390
222 K A -2.5525
223 S A -1.8504
224 C A -1.6642
225 D A -2.8108
226 K A -2.7755
227 T A -1.8818
228 H A -1.8455
1 D B -2.4061
2 I B 0.0000
3 Q B -2.2778
4 M B 0.0000
5 T B -1.3896
6 Q B 0.0000
7 S B -0.6241
8 P B -0.6210
9 S B -0.9003
10 A B -0.7881
11 M B -0.6133
12 S B -0.8871
13 A B -1.0391
14 S B -1.0282
15 V B -0.3209
16 G B -0.9756
17 D B -1.8913
18 R B -2.4119
19 V B 0.0000
20 T B -0.6544
21 I B 0.0000
22 T B -0.8920
23 C B 0.0000
24 R B -2.6990
25 A B 0.0000
26 S B -2.0889
27 Q B -2.3927
28 G B -1.7257
29 I B 0.0000
30 S B -0.9620
31 H B -0.8760
32 Y B -0.1833
33 L B 0.0000
34 V B 0.0000
35 W B 0.0000
36 F B 0.0000
37 Q B 0.0000
38 Q B 0.0000
39 K B -1.7625
40 P B -1.3744
41 G B -1.6841
42 K B -2.1726
43 V B -0.9719
44 P B 0.0000
45 K B -1.4302
46 R B 0.0000
47 L B 0.0000
48 I B 0.0000
49 Y B -0.1240
50 A B -0.2870
51 A B 0.0000
52 S B -0.3370
53 S B -0.0408
54 L B 0.2255
55 Q B -0.3953
56 S B -0.4378
57 G B -0.5107
58 V B -0.3610
59 P B -0.3500
60 S B -0.4538
61 R B -0.7780
62 F B 0.0000
63 S B -0.3435
64 G B -0.2849
65 S B -0.8892
66 G B -1.4239
67 S B -1.3789
68 G B -1.5239
69 T B -2.1640
70 E B -2.8944
71 F B 0.0000
72 T B -0.8843
73 L B 0.0000
74 T B -0.6270
75 I B 0.0000
76 S B -1.3843
77 S B -1.2917
78 L B 0.0000
79 Q B -0.7842
80 P B -1.4342
81 E B -1.7297
82 D B 0.0000
83 F B -1.2378
84 A B 0.0000
85 T B 0.0000
86 Y B 0.0000
87 Y B 0.0000
88 C B 0.0000
89 L B 0.0000
90 Q B 0.0000
91 H B 0.0000
92 N B -0.4780
93 S B -0.5276
94 Y B 0.0844
95 P B -0.3919
96 W B 0.0000
97 T B -0.7586
98 F B -0.4888
99 G B 0.0000
100 Q B -1.9007
101 G B 0.0000
102 T B 0.0000
103 K B -1.9450
104 V B 0.0000
105 E B -1.2622
106 I B 0.0000
107 K B -1.3637
108 R B -0.9888
109 T B -0.1618
110 V B 0.3316
111 A B -0.0139
112 A B -0.1245
113 P B 0.0000
114 S B -0.2227
115 V B 0.0000
116 F B 0.0000
117 I B 0.0000
118 F B 0.0000
119 P B -0.5141
120 P B 0.0000
121 S B -1.8185
122 D B -3.1136
123 E B -3.0019
124 Q B 0.0000
125 L B -2.2713
126 K B -2.8559
127 S B -1.7746
128 G B -1.2502
129 T B -0.9727
130 A B 0.0000
131 S B 0.0000
132 V B 0.0000
133 V B 0.0000
134 C B 0.0000
135 L B 0.0000
136 L B 0.0000
137 N B 0.0000
138 N B -0.8356
139 F B 0.0000
140 Y B 0.0000
141 P B -1.4340
142 R B -2.3259
143 E B -2.9006
144 A B -2.1647
145 K B -2.3927
146 V B -1.0712
147 Q B -0.6518
148 W B 0.0000
149 K B -0.5252
150 V B 0.0000
151 D B -1.8854
152 N B -1.5129
153 A B -0.2711
154 L B 0.6331
155 Q B -0.3683
156 S B -0.6836
157 G B -1.2640
158 N B -1.5619
159 S B -1.3784
160 Q B -1.2741
161 E B -1.3879
162 S B -0.7516
163 V B -0.6055
164 T B 0.0000
165 E B -2.0173
166 Q B 0.0000
167 D B -1.9731
168 S B -2.0841
169 K B -2.4205
170 D B -1.6334
171 S B 0.0000
172 T B 0.0000
173 Y B 0.0000
174 S B 0.0000
175 L B 0.0000
176 S B 0.0000
177 S B 0.0000
178 T B -0.6304
179 L B 0.0000
180 T B -0.5964
181 L B -0.7072
182 S B -0.9103
183 K B -1.8973
184 A B -1.6777
185 D B -2.2139
186 Y B 0.0000
187 E B -3.2824
188 K B -3.4651
189 H B -2.8962
190 K B -3.2310
191 V B -1.4145
192 Y B 0.0000
193 A B -0.4938
194 C B 0.0000
195 E B -0.5421
196 V B 0.0000
197 T B -1.2298
198 H B 0.0000
199 Q B -1.6933
200 G B -0.4325
201 L B -0.2462
202 S B -0.4585
203 S B -0.4352
204 P B -0.5408
205 V B 0.1160
206 T B -0.2770
207 K B -0.5727
208 S B -0.5534
209 F B 0.0000
210 N B -1.7422
211 R B -2.3559
212 G B -1.8759
213 E B -2.0871
214 C B -1.2414
Download PDB file
View in 3Dmol
Play the video

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
YE57A -1.2557 -0.0176 View CSV PDB
YR57A -0.7998 -0.0224 View CSV PDB
VR5A -0.7013 -0.0182 View CSV PDB
VK5A -0.7363 -0.0144 View CSV PDB
YK102A -0.2598 -0.0175 View CSV PDB
LK178A -0.0071 -0.0229 View CSV PDB
YR102A -0.1069 -0.0146 View CSV PDB
LR178A 0.0761 -0.0269 View CSV PDB
IR58A 0.095 -0.0104 View CSV PDB
IK58A 0.5656 -0.015 View CSV PDB
YK59A 1.3139 -0.0095 View CSV PDB
YR59A 1.9791 -0.0109 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018