Project name: EGF14_A564T_Dynamic [mutate: AT58A]

Status: done

Started: 2025-03-07 23:35:11
Chain sequence(s) A: DVDECASTPCRNGAKCVDQPDGYECRCAEGFEGTLCDRNVDDCSPDPCHHGRCVDGIASFSCACAPGYTGTRCESQVDECRSQPCRHGGKCLDLVDKYLCRCPSGTTGVNCEVNIDDCASNPCTFGVCRDGINRYDCVCQPGFTGPLCNVEINECASSPCGEGGSCVDGENGFRCLCPPGSLPPLCLPPSHPCAHEPCSHGICYDAPGGFRCVCEPGWSGPRCS
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues AT58A
Energy difference between WT (input) and mutated protein (by FoldX) 2.75854 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:02:05)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:10)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:27:21)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:27:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:27:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:27:23)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:27:24)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:27:25)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:27:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:27:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:27:27)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:27:27)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:27:28)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:27:29)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:27:29)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:27:31)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:32)
Show buried residues
Minimal score value
-3.5921
Maximal score value
2.4437
Average score
-0.7992
Total score value
-179.0283
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 D A -2.4292
2 V A 0.0000
3 D A -3.5921
4 E A -3.4817
5 C A -1.5857
6 A A -0.9887
7 S A -1.3186
8 T A -0.8371
9 P A -1.2955
10 C A -1.6341
11 R A -2.1448
12 N A -1.9322
13 G A -1.5420
14 A A -1.6083
15 K A -2.0671
16 C A -1.3527
17 V A -1.2582
18 D A -2.9485
19 Q A -2.3994
20 P A -2.0855
21 D A -3.5163
22 G A 0.0000
23 Y A 0.0000
24 E A -2.3265
25 C A 0.0000
26 R A -2.2617
27 C A 0.0000
28 A A -1.5101
29 E A -2.6466
30 G A -1.5576
31 F A -1.4236
32 E A -2.5669
33 G A -1.9631
34 T A -1.3921
35 L A -1.2428
36 C A 0.0000
37 D A -2.5566
38 R A -2.4992
39 N A -2.0286
40 V A -0.8007
41 D A -2.3929
42 D A -2.3352
43 C A -0.9970
44 S A -1.3538
45 P A -0.8235
46 D A -1.2354
47 P A -0.8123
48 C A -0.0616
49 H A -1.5202
50 H A -1.9711
51 G A -1.4629
52 R A -1.7841
53 C A -0.6580
54 V A 0.4083
55 D A -0.7989
56 G A 0.0953
57 I A 1.2557
58 T A 0.2054 mutated: AT58A
59 S A 0.0600
60 F A 0.0558
61 S A -0.3853
62 C A 0.0000
63 A A -0.5283
64 C A -0.3728
65 A A 0.0977
66 P A 0.0593
67 G A -0.0764
68 Y A 0.6062
69 T A 0.0000
70 G A -0.6334
71 T A -0.9270
72 R A -1.5909
73 C A -0.9476
74 E A -2.1615
75 S A -1.6420
76 Q A -1.3568
77 V A -1.1399
78 D A -2.5240
79 E A -1.8541
80 C A 0.0000
81 R A -2.6839
82 S A -1.9034
83 Q A -1.6079
84 P A -1.2033
85 C A -1.7795
86 R A -2.6157
87 H A -2.0275
88 G A -1.7541
89 G A -2.0246
90 K A -2.4904
91 C A -1.4075
92 L A 0.1624
93 D A -0.3048
94 L A 1.4761
95 V A 0.7899
96 D A -1.9476
97 K A -0.9950
98 Y A -0.2389
99 L A 0.3152
100 C A -0.9482
101 R A -2.1443
102 C A -1.8986
103 P A -1.4792
104 S A -1.2909
105 G A -1.1027
106 T A -1.0235
107 T A -0.6959
108 G A -0.4973
109 V A 0.9550
110 N A -0.6243
111 C A 0.0356
112 E A -1.6844
113 V A 0.0000
114 N A -2.4211
115 I A -2.0729
116 D A -2.8216
117 D A -2.7157
118 C A 0.0000
119 A A -0.9825
120 S A -0.8478
121 N A -0.7046
122 P A -0.0716
123 C A 1.1501
124 T A 0.9569
125 F A 2.4437
126 G A 1.4060
127 V A 1.7171
128 C A 0.1206
129 R A -2.4301
130 D A -2.8400
131 G A -1.3137
132 I A 0.3746
133 N A -2.1615
134 R A -2.2118
135 Y A 0.0000
136 D A -0.9853
137 C A 0.0000
138 V A 2.2969
139 C A 0.0000
140 Q A 0.0000
141 P A -0.0541
142 G A 0.2173
143 F A 0.0000
144 T A 0.6926
145 G A 0.0000
146 P A 0.0085
147 L A 0.6174
148 C A 0.0000
149 N A -0.4441
150 V A 1.1309
151 E A 0.6999
152 I A 1.3664
153 N A 0.0000
154 E A -1.1976
155 C A 0.0000
156 A A 0.2107
157 S A 0.0388
158 S A 0.0000
159 P A -0.1776
160 C A -0.3739
161 G A -0.9430
162 E A -1.2642
163 G A -1.1337
164 G A -0.7568
165 S A 0.0000
166 C A 0.2886
167 V A -0.2804
168 D A -2.1002
169 G A -2.2661
170 E A -2.8374
171 N A -2.3203
172 G A -2.0170
173 F A -1.4529
174 R A -0.7976
175 C A 0.0000
176 L A 0.7718
177 C A 0.7871
178 P A -0.0927
179 P A -0.4466
180 G A -0.5337
181 S A -0.1949
182 L A 0.0000
183 P A -0.3565
184 P A -0.5209
185 L A 0.0000
186 C A 0.1315
187 L A 0.3068
188 P A 0.0000
189 P A -0.6076
190 S A -0.4101
191 H A -0.2248
192 P A -0.1434
193 C A 0.0000
194 A A -0.7236
195 H A -1.5834
196 E A -2.2105
197 P A -1.0868
198 C A 0.0000
199 S A -0.9138
200 H A -0.5678
201 G A 0.0000
202 I A 0.0000
203 C A 0.0000
204 Y A 0.0437
205 D A -0.6419
206 A A -0.4595
207 P A -0.3947
208 G A -0.3949
209 G A -0.0747
210 F A 0.7137
211 R A -0.6511
212 C A 0.1244
213 V A 0.3781
214 C A -0.3272
215 E A -0.9248
216 P A -1.0035
217 G A -0.9937
218 W A -0.6295
219 S A -0.6148
220 G A -0.7334
221 P A -0.7435
222 R A -0.7355
223 C A 0.0872
224 S A -0.2365
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.7992 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_11 -0.7992 View CSV PDB
model_10 -0.8448 View CSV PDB
model_2 -0.8594 View CSV PDB
model_1 -0.8625 View CSV PDB
model_7 -0.8719 View CSV PDB
CABS_average -0.9321 View CSV PDB
model_5 -0.9612 View CSV PDB
model_8 -0.9706 View CSV PDB
model_0 -0.9747 View CSV PDB
model_9 -0.9753 View CSV PDB
model_6 -1.0 View CSV PDB
model_3 -1.0161 View CSV PDB
model_4 -1.0497 View CSV PDB
input -1.1953 View CSV PDB