Project name: F2B_scFv

Status: done

Started: 2026-05-29 06:45:33
Chain sequence(s) A: EVQLVESGGGLVQPGRSLRLSCAASGFTFDDYAMHWVRQAPGKGLEWVSGISWNSGSIGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYYCAKDSRGYGDYRLGGAYWGQGTLVTVSSGGGGSGGGGSGGGGSEIVMTQSPATLSVSPGERATLSCRASQSVSSNLAWYQQKPGQAPRLLIYGASTRATGIPARFSGSGSGTEFTLTISSLQSEDFAVYYCQQYNNWPWTFGQGTKVEIK
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                                          (00:01:51)
[INFO]       AutoMutEv:Residue number 11 from chain A and a score of 1.452 (leucine) selected for  
                       automated mutation                                                          (00:01:52)
[INFO]       AutoMutEv:Residue number 58 from chain A and a score of 1.194 (isoleucine) selected   
                       for automated mutation                                                      (00:01:52)
[INFO]       AutoMutEv:Residue number 5 from chain A and a score of 1.172 (valine) selected for    
                       automated mutation                                                          (00:01:52)
[INFO]       AutoMutEv:Residue number 118 from chain A and a score of 0.996 (leucine) selected for 
                       automated mutation                                                          (00:01:52)
[INFO]       AutoMutEv:Residue number 244 from chain A and a score of 0.806 (isoleucine) selected  
                       for automated mutation                                                      (00:01:52)
[INFO]       AutoMutEv:Residue number 103 from chain A and a score of 0.695 (tyrosine) selected    
                       for automated mutation                                                      (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 11 from chain A (leucine) into methionine           (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 5 from chain A (valine) into threonine              (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 58 from chain A (isoleucine) into methionine        (00:01:52)
[INFO]       AutoMutEv:Mutating residue number 58 from chain A (isoleucine) into threonine         (00:01:58)
[INFO]       AutoMutEv:Mutating residue number 5 from chain A (valine) into alanine                (00:01:58)
[INFO]       AutoMutEv:Mutating residue number 58 from chain A (isoleucine) into leucine           (00:01:59)
[INFO]       AutoMutEv:Mutating residue number 5 from chain A (valine) into methionine             (00:02:03)
[INFO]       AutoMutEv:Mutating residue number 244 from chain A (isoleucine) into threonine        (00:02:04)
[INFO]       AutoMutEv:Mutating residue number 244 from chain A (isoleucine) into leucine          (00:02:05)
[INFO]       AutoMutEv:Mutating residue number 103 from chain A (tyrosine) into histidine          (00:02:10)
[INFO]       AutoMutEv:Mutating residue number 244 from chain A (isoleucine) into methionine       (00:02:10)
[INFO]       AutoMutEv:Mutating residue number 118 from chain A (leucine) into methionine          (00:02:13)
[INFO]       AutoMutEv:Mutating residue number 103 from chain A (tyrosine) into cysteine           (00:02:15)
[INFO]       AutoMutEv:Mutating residue number 103 from chain A (tyrosine) into tryptophan         (00:02:21)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain A (leucine) into            
                       methionine: Energy difference: -0.0794 kcal/mol, Difference in average      
                       score from the base case: -0.0066                                           (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 58 from chain A (isoleucine) into         
                       threonine: Energy difference: 1.1828 kcal/mol, Difference in average score  
                       from the base case: -0.0223                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 58 from chain A (isoleucine) into         
                       methionine: Energy difference: 0.4612 kcal/mol, Difference in average score 
                       from the base case: -0.0107                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 58 from chain A (isoleucine) into         
                       leucine: Energy difference: -0.0498 kcal/mol, Difference in average score   
                       from the base case: -0.0080                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into threonine:   
                       Energy difference: 0.0413 kcal/mol, Difference in average score from the    
                       base case: -0.0196                                                          (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into alanine:     
                       Energy difference: 0.5950 kcal/mol, Difference in average score from the    
                       base case: -0.0188                                                          (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into methionine:  
                       Energy difference: -0.5805 kcal/mol, Difference in average score from the   
                       base case: -0.0111                                                          (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 118 from chain A (leucine) into           
                       methionine: Energy difference: 0.0561 kcal/mol, Difference in average score 
                       from the base case: -0.0069                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 244 from chain A (isoleucine) into        
                       threonine: Energy difference: 0.5770 kcal/mol, Difference in average score  
                       from the base case: -0.0298                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 244 from chain A (isoleucine) into        
                       methionine: Energy difference: -0.2290 kcal/mol, Difference in average      
                       score from the base case: -0.0128                                           (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 244 from chain A (isoleucine) into        
                       leucine: Energy difference: -0.0463 kcal/mol, Difference in average score   
                       from the base case: -0.0066                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 103 from chain A (tyrosine) into          
                       histidine: Energy difference: 0.0763 kcal/mol, Difference in average score  
                       from the base case: -0.0313                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 103 from chain A (tyrosine) into          
                       cysteine: Energy difference: 0.0263 kcal/mol, Difference in average score   
                       from the base case: -0.0041                                                 (00:02:27)
[INFO]       AutoMutEv:Effect of mutation residue number 103 from chain A (tyrosine) into          
                       tryptophan: Energy difference: 0.0013 kcal/mol, Difference in average score 
                       from the base case: -0.0012                                                 (00:02:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:32)
Show buried residues
Minimal score value
-2.8808
Maximal score value
1.4523
Average score
-0.6619
Total score value
-162.1659
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 -2.1980
2 V A -1.4135
3 Q A -1.3820
4 L A 0.0000
5 V A 1.1716
6 E A 0.0000
7 S A -0.2323
8 G A -0.8694
9 G A -0.0822
10 G A 0.5221
11 L A 1.4523
12 V A -0.3017
13 Q A -1.5604
14 P A -1.9755
15 G A -2.1301
16 R A -2.7246
17 S A -2.0835
18 L A -1.2959
19 R A -2.1255
20 L A 0.0000
21 S A -0.3728
22 C A 0.0000
23 A A -0.0437
24 A A 0.0000
25 S A -1.0704
26 G A -1.3431
27 F A -0.7774
28 T A -0.5036
29 F A 0.0000
30 D A -1.6691
31 D A -0.9897
32 Y A 0.0000
33 A A -0.2790
34 M A 0.0000
35 H A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.7832
40 A A -1.1530
41 P A -1.0063
42 G A -1.4519
43 K A -2.4254
44 G A -1.6296
45 L A 0.0000
46 E A -1.2599
47 W A 0.0000
48 V A 0.0000
49 S A 0.0000
50 G A 0.0000
51 I A 0.0000
52 S A -0.3023
53 W A -0.8793
54 N A -1.5212
55 S A -0.8225
56 G A -0.5895
57 S A 0.1349
58 I A 1.1941
59 G A 0.3891
60 Y A -0.4596
61 A A -1.4056
62 D A -2.6823
63 S A -1.9456
64 V A 0.0000
65 K A -2.5989
66 G A -1.7512
67 R A -1.5312
68 F A 0.0000
69 T A -0.6661
70 I A 0.0000
71 S A -0.1871
72 R A -1.1425
73 D A -1.6035
74 N A -2.0854
75 A A -1.5078
76 K A -2.2718
77 N A -1.8740
78 S A 0.0000
79 L A 0.0000
80 Y A -0.5289
81 L A 0.0000
82 Q A -1.2614
83 M A 0.0000
84 N A -1.9467
85 S A -1.7775
86 L A 0.0000
87 R A -2.5859
88 A A -1.8028
89 E A -2.4680
90 D A 0.0000
91 T A -0.4892
92 A A 0.0000
93 L A 0.4513
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 K A 0.0000
99 D A 0.0000
100 S A 0.0000
101 R A -0.9044
102 G A -0.3514
103 Y A 0.6954
104 G A -0.1142
105 D A -0.3229
106 Y A 0.2204
107 R A -1.3778
108 L A -0.4817
109 G A -0.5139
110 G A 0.0000
111 A A 0.0000
112 Y A 0.0085
113 W A -0.1660
114 G A 0.0000
115 Q A -1.1104
116 G A 0.0000
117 T A 0.3309
118 L A 0.9963
119 V A 0.0000
120 T A 0.3068
121 V A 0.0000
122 S A -0.8566
123 S A -1.0343
124 G A -1.1000
125 G A -1.1045
126 G A -1.1642
127 G A -1.1639
128 S A -0.9288
129 G A -1.3672
130 G A -1.3838
131 G A -1.4875
132 G A -1.1202
133 S A -1.0034
134 G A -1.1369
135 G A -1.7251
136 G A -1.5727
137 G A -1.7013
138 S A -1.2787
139 E A -1.7416
140 I A 0.0000
141 V A 0.6833
142 M A 0.0000
143 T A -0.6636
144 Q A 0.0000
145 S A -0.7089
146 P A -0.3281
147 A A -0.4717
148 T A -0.4831
149 L A -0.1759
150 S A -0.3782
151 V A 0.0000
152 S A -1.2123
153 P A -1.4500
154 G A -1.9532
155 E A -2.7858
156 R A -2.8808
157 A A 0.0000
158 T A -0.5508
159 L A 0.0000
160 S A -0.9037
161 C A 0.0000
162 R A -2.2857
163 A A 0.0000
164 S A -1.0431
165 Q A -1.7525
166 S A -1.5142
167 V A 0.0000
168 S A -0.9818
169 S A -0.8749
170 N A -0.8555
171 L A 0.0000
172 A A 0.0000
173 W A 0.0000
174 Y A 0.0000
175 Q A 0.0000
176 Q A 0.0000
177 K A -1.4837
178 P A -1.0345
179 G A -1.4742
180 Q A -2.1416
181 A A -1.4098
182 P A 0.0000
183 R A -1.2967
184 L A -0.4540
185 L A 0.0000
186 I A 0.0000
187 Y A -0.2646
188 G A -0.5587
189 A A 0.0000
190 S A -0.7157
191 T A -0.6743
192 R A -1.0847
193 A A 0.0000
194 T A -0.6840
195 G A -0.6453
196 I A 0.0000
197 P A -0.4232
198 A A -0.3815
199 R A -0.7059
200 F A 0.0000
201 S A -0.5684
202 G A 0.0000
203 S A -0.7557
204 G A -1.2661
205 S A -1.2776
206 G A -1.3826
207 T A -1.9655
208 E A -2.6749
209 F A 0.0000
210 T A -0.8599
211 L A 0.0000
212 T A -0.6020
213 I A 0.0000
214 S A -1.4539
215 S A -1.8078
216 L A 0.0000
217 Q A -1.5746
218 S A -0.8598
219 E A -1.3862
220 D A 0.0000
221 F A -0.1783
222 A A 0.0000
223 V A -0.3229
224 Y A 0.0000
225 Y A 0.0000
226 C A 0.0000
227 Q A 0.0000
228 Q A 0.0000
229 Y A 0.0000
230 N A -1.0539
231 N A -1.1002
232 W A -0.2044
233 P A -0.6868
234 W A 0.0000
235 T A 0.0000
236 F A -0.0102
237 G A 0.0000
238 Q A -1.4849
239 G A 0.0000
240 T A 0.0000
241 K A -1.2176
242 V A 0.0000
243 E A -0.1870
244 I A 0.8065
245 K A -0.9281
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
VM5A -0.5805 -0.0111 View CSV PDB
IM244A -0.229 -0.0128 View CSV PDB
IL58A -0.0498 -0.008 View CSV PDB
LM11A -0.0794 -0.0066 View CSV PDB
IL244A -0.0463 -0.0066 View CSV PDB
YW103A 0.0013 -0.0012 View CSV PDB
VT5A 0.0413 -0.0196 View CSV PDB
YH103A 0.0763 -0.0313 View CSV PDB
LM118A 0.0561 -0.0069 View CSV PDB
IM58A 0.4612 -0.0107 View CSV PDB