Project name: GFP_evolmut

Status: done

Started: 2024-03-11 09:08:51
Chain sequence(s) A: KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTTTVQCFSRYPDHMKRHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITH
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                                          (00:03:06)
[INFO]       AutoMutEv:Residue number 11 from chain A and a score of 1.359 (valine) selected for   
                       automated mutation                                                          (00:03:08)
[INFO]       AutoMutEv:Residue number 39 from chain A and a score of 0.901 (tyrosine) selected for 
                       automated mutation                                                          (00:03:08)
[INFO]       AutoMutEv:Residue number 10 from chain A and a score of 0.527 (glycine) selected for  
                       automated mutation                                                          (00:03:08)
[INFO]       AutoMutEv:Residue number 221 from chain A and a score of 0.351 (leucine) selected for 
                       automated mutation                                                          (00:03:08)
[INFO]       AutoMutEv:Residue number 38 from chain A and a score of 0.176 (threonine) selected    
                       for automated mutation                                                      (00:03:08)
[INFO]       AutoMutEv:Residue number 176 from chain A and a score of 0.141 (valine) selected for  
                       automated mutation                                                          (00:03:08)
[INFO]       AutoMutEv:Mutating residue number 11 from chain A (valine) into threonine             (00:03:08)
[INFO]       AutoMutEv:Mutating residue number 39 from chain A (tyrosine) into cysteine            (00:03:08)
[INFO]       AutoMutEv:Mutating residue number 11 from chain A (valine) into methionine            (00:03:08)
[INFO]       AutoMutEv:Mutating residue number 11 from chain A (valine) into alanine               (00:04:34)
[INFO]       AutoMutEv:Mutating residue number 39 from chain A (tyrosine) into histidine           (00:04:37)
[INFO]       AutoMutEv:Mutating residue number 39 from chain A (tyrosine) into tryptophan          (00:04:37)
[INFO]       AutoMutEv:Mutating residue number 10 from chain A (glycine) into glutamic acid        (00:06:01)
[INFO]       AutoMutEv:Mutating residue number 10 from chain A (glycine) into asparagine           (00:06:07)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (threonine) into glutamic acid      (00:06:08)
[INFO]       AutoMutEv:Mutating residue number 10 from chain A (glycine) into aspartic acid        (00:07:35)
[INFO]       AutoMutEv:Mutating residue number 221 from chain A (leucine) into methionine          (00:07:36)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (threonine) into aspartic acid      (00:07:40)
[INFO]       AutoMutEv:Mutating residue number 38 from chain A (threonine) into lysine             (00:09:06)
[INFO]       AutoMutEv:Mutating residue number 176 from chain A (valine) into alanine              (00:09:09)
[INFO]       AutoMutEv:Mutating residue number 176 from chain A (valine) into methionine           (00:10:41)
[INFO]       AutoMutEv:Mutating residue number 176 from chain A (valine) into threonine            (00:10:44)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain A (valine) into threonine:  
                       Energy difference: 0.2298 kcal/mol, Difference in average score from the    
                       base case: -0.0274                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain A (valine) into alanine:    
                       Energy difference: 0.3459 kcal/mol, Difference in average score from the    
                       base case: -0.0318                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 11 from chain A (valine) into methionine: 
                       Energy difference: -0.4750 kcal/mol, Difference in average score from the   
                       base case: -0.0080                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 39 from chain A (tyrosine) into           
                       histidine: Energy difference: 0.5381 kcal/mol, Difference in average score  
                       from the base case: -0.0296                                                 (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 39 from chain A (tyrosine) into cysteine: 
                       Energy difference: 0.5601 kcal/mol, Difference in average score from the    
                       base case: -0.0073                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 39 from chain A (tyrosine) into           
                       tryptophan: Energy difference: 1.0351 kcal/mol, Difference in average score 
                       from the base case: 0.0032                                                  (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into glutamic   
                       acid: Energy difference: 2.4484 kcal/mol, Difference in average score from  
                       the base case: -0.0252                                                      (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into aspartic   
                       acid: Energy difference: 0.0250 kcal/mol, Difference in average score from  
                       the base case: -0.0265                                                      (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into            
                       asparagine: Energy difference: 1.0717 kcal/mol, Difference in average score 
                       from the base case: -0.0150                                                 (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 221 from chain A (leucine) into           
                       methionine: Energy difference: 0.0306 kcal/mol, Difference in average score 
                       from the base case: 0.0023                                                  (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (threonine) into glutamic 
                       acid: Energy difference: 0.1227 kcal/mol, Difference in average score from  
                       the base case: -0.0215                                                      (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (threonine) into aspartic 
                       acid: Energy difference: 0.1862 kcal/mol, Difference in average score from  
                       the base case: -0.0237                                                      (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 38 from chain A (threonine) into lysine:  
                       Energy difference: -0.3171 kcal/mol, Difference in average score from the   
                       base case: -0.0223                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 176 from chain A (valine) into threonine: 
                       Energy difference: 0.3612 kcal/mol, Difference in average score from the    
                       base case: -0.0243                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 176 from chain A (valine) into alanine:   
                       Energy difference: 1.0718 kcal/mol, Difference in average score from the    
                       base case: -0.0427                                                          (00:12:20)
[INFO]       AutoMutEv:Effect of mutation residue number 176 from chain A (valine) into            
                       methionine: Energy difference: -0.4162 kcal/mol, Difference in average      
                       score from the base case: -0.0290                                           (00:12:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:27)
Show buried residues
Minimal score value
-4.216
Maximal score value
1.3585
Average score
-1.0282
Total score value
-232.3666
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
3 K A -2.4336
4 G A 0.0000
5 E A -2.4002
6 E A -2.4765
7 L A -0.8666
8 F A 0.0000
9 T A -0.2401
10 G A 0.5274
11 V A 1.3585
12 V A 0.0000
13 P A -0.9415
14 I A 0.0000
15 L A -1.3174
16 V A 0.0000
17 E A -2.5537
18 L A 0.0000
19 D A -3.5794
20 G A 0.0000
21 D A -2.8287
22 V A 0.0000
23 N A -2.1384
24 G A -1.7489
25 H A -2.3107
26 K A -3.0339
27 F A 0.0000
28 S A -1.8958
29 V A 0.0000
30 S A -1.2551
31 G A 0.0000
32 E A -2.2825
33 G A -1.6876
34 E A -1.4665
35 G A 0.0000
36 D A 0.0458
37 A A 0.0000
38 T A 0.1759
39 Y A 0.9007
40 G A 0.0000
41 K A -0.4318
42 L A 0.0000
43 T A -0.7877
44 L A 0.0000
45 K A -1.2022
46 F A 0.0000
47 I A -0.9503
48 C A 0.0000
49 T A -1.0388
50 T A -1.3307
51 G A -1.6443
52 K A -2.2753
53 L A 0.0000
54 P A -1.2457
55 V A 0.0000
56 P A -0.7489
57 W A 0.0000
58 P A 0.0000
59 T A 0.0000
60 L A 0.0000
61 V A 0.0000
62 T A -0.0001
63 T A 0.0000
64 L A 0.0000
68 V A 0.0030
69 Q A -0.1839
70 C A 0.0000
71 F A 0.0000
72 S A 0.0000
73 R A -1.3559
74 Y A 0.0000
75 P A -1.9148
76 D A -2.8557
77 H A -2.1443
78 M A 0.0000
79 K A -2.8430
80 R A -2.8515
81 H A -1.7268
82 D A 0.0000
83 F A 0.0000
84 F A 0.0000
85 K A 0.0000
86 S A -1.1974
87 A A 0.0000
88 M A 0.0000
89 P A -1.6059
90 E A -2.1584
91 G A 0.0000
92 Y A 0.0000
93 V A -0.7676
94 Q A 0.0000
95 E A -2.2978
96 R A 0.0000
97 T A -1.0357
98 I A 0.0000
99 S A -1.2772
100 F A 0.0000
101 K A -2.5200
102 D A -2.9225
103 D A -2.8662
104 G A 0.0000
105 N A -1.5582
106 Y A 0.0000
107 K A -2.5103
108 T A 0.0000
109 R A -3.3411
110 A A 0.0000
111 E A -2.2234
112 V A 0.0000
113 K A -1.6465
114 F A -1.8879
115 E A -2.6978
116 G A -2.2653
117 D A -2.3927
118 T A -1.5606
119 L A 0.0000
120 V A 0.0000
121 N A 0.0000
122 R A -3.2473
123 I A 0.0000
124 E A -4.2160
125 L A 0.0000
126 K A -3.0971
127 G A 0.0000
128 I A -1.2638
129 D A -2.2926
130 F A 0.0000
131 K A -3.9588
132 E A -4.0000
133 D A -3.6505
134 G A -2.8598
135 N A -2.3198
136 I A 0.0000
137 L A -2.0519
138 G A -2.3805
139 H A -2.2785
140 K A -2.6063
141 L A -1.9389
142 E A -2.4041
143 Y A -1.0366
144 N A -0.7138
145 Y A -0.8030
146 N A -1.0062
147 S A -1.0636
148 H A 0.0000
149 N A -1.4579
150 V A 0.0000
151 Y A -0.0378
152 I A 0.0000
153 T A -1.1414
154 A A -1.7187
155 D A -2.2308
156 K A -3.2066
157 Q A -3.1688
158 K A -3.2478
159 N A -2.8733
160 G A 0.0000
161 I A 0.0000
162 K A -1.0662
163 A A 0.0000
164 N A -1.2525
165 F A 0.0000
166 K A -1.7957
167 I A 0.0000
168 R A -1.1128
169 H A 0.0000
170 N A -1.4386
171 I A 0.0000
172 E A -3.4518
173 D A -3.0614
174 G A -1.8692
175 S A -0.7908
176 V A 0.1405
177 Q A 0.0000
178 L A -0.8987
179 A A 0.0000
180 D A -1.4265
181 H A 0.0000
182 Y A -0.3334
183 Q A 0.0000
184 Q A -1.0804
185 N A 0.0000
186 T A -0.7355
187 P A -0.8271
188 I A -0.2234
189 G A -1.2460
190 D A -2.0978
191 G A -1.4762
192 P A -0.8002
193 V A -0.1090
194 L A -0.2339
195 L A -0.6331
196 P A 0.0000
197 D A -2.4700
198 N A -1.8735
199 H A 0.0000
200 Y A -0.3092
201 L A 0.0000
202 S A -0.7247
203 T A -0.9611
204 Q A -1.3144
205 S A -0.5270
206 A A 0.0076
207 L A -0.0820
208 S A -0.7119
209 K A -1.9732
210 D A -2.1264
211 P A -1.8268
212 N A -2.4818
213 E A -2.7197
214 K A -3.3442
215 R A -3.3788
216 D A -2.2940
217 H A 0.0000
218 M A 0.0000
219 V A -0.3543
220 L A 0.0000
221 L A 0.3512
222 E A -0.2313
223 F A 0.0155
224 V A 0.0000
225 T A -0.5279
226 A A 0.0000
227 A A -0.4296
228 G A -0.6645
229 I A -0.7235
230 T A -0.5736
231 H A -1.3156
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
VM176A -0.4162 -0.029 View CSV PDB
TK38A -0.3171 -0.0223 View CSV PDB
VM11A -0.475 -0.008 View CSV PDB
GD10A 0.025 -0.0265 View CSV PDB
TE38A 0.1227 -0.0215 View CSV PDB
VT11A 0.2298 -0.0274 View CSV PDB
VT176A 0.3612 -0.0243 View CSV PDB
YH39A 0.5381 -0.0296 View CSV PDB
GN10A 1.0717 -0.015 View CSV PDB
YC39A 0.5601 -0.0073 View CSV PDB
LM221A 0.0306 0.0023 View CSV PDB