Project name: PTx S2 V1 [mutate: FA79A, VA157A, YA156A, SA161A]

Status: done

Started: 2025-04-27 17:18:14
Chain sequence(s) A: TPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYVSKYEELKKKLEEVYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC
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 VA157A,YA156A,SA161A,FA79A
Energy difference between WT (input) and mutated protein (by FoldX) -0.118607 kcal/mol
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                                                       (00:03:35)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:39)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:26:22)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:26:23)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:26:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:26:24)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:26:24)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:26:25)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:26:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:26:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:26:27)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:26:27)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:26:28)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:26:28)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:26:29)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:26:32)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:33)
Show buried residues
Minimal score value
-3.0274
Maximal score value
1.5998
Average score
-0.5854
Total score value
-115.9086
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 T A -0.0956
2 P A -0.3968
3 G A -0.5202
4 I A 0.2276
5 V A 0.0000
6 I A 1.5998
7 P A 0.1089
8 P A -0.9877
9 Q A -1.6994
10 E A -2.3409
11 Q A -1.7087
12 I A -0.8559
13 T A 0.0000
14 Q A 0.0000
15 H A -1.5870
16 G A -1.0861
17 S A 0.0000
18 P A -0.6642
19 Y A -0.5029
20 G A -1.2385
21 R A -2.2098
22 C A -1.1363
23 A A -0.8179
24 N A -1.1974
25 K A -0.5249
26 T A -0.3507
27 R A 0.0000
28 A A 0.3150
29 L A 0.0000
30 T A 0.0000
31 V A 0.0000
32 A A -1.0198
33 E A 0.0000
34 L A 0.0000
35 R A -2.4530
36 G A -1.6706
37 S A -1.5219
38 G A -1.6307
39 D A -1.5954
40 L A -1.3458
41 Q A -2.0457
42 E A -2.2064
43 Y A -0.6151
44 L A 0.0000
45 R A -2.5421
46 H A -1.8168
47 V A -0.8074
48 T A -0.6867
49 R A 0.0000
50 G A -0.2356
51 W A 0.2343
52 S A -0.0447
53 I A 0.3829
54 F A 0.0000
55 A A 0.0000
56 L A 0.0000
57 Y A 0.7812
58 D A -0.6241
59 G A 0.0000
60 T A -0.3173
61 Y A 0.0000
62 L A 0.4514
63 G A 0.0000
64 G A -1.2838
65 E A -2.0106
66 Y A -0.6650
67 G A -0.3030
68 G A 0.1798
69 V A 1.2736
70 I A -0.1534
71 K A -1.8939
72 D A -2.4512
73 G A -1.7249
74 T A -1.2413
75 P A -0.7328
76 G A -0.8495
77 G A -1.3066
78 A A 0.0000
79 A A -1.0448 mutated: FA79A
80 D A -1.9469
81 L A -0.8454
82 K A -1.9138
83 T A 0.0000
84 T A -0.4969
85 F A 0.0000
86 C A 0.0000
87 I A 0.0000
88 M A 0.0000
89 T A 0.0000
90 T A 0.0000
91 R A -2.1944
92 N A -2.8581
93 T A -2.0351
94 G A -2.1167
95 Q A -1.5759
96 P A -0.8755
97 A A -0.4758
98 T A -0.8877
99 D A -0.5022
100 H A 0.1693
101 Y A 0.8620
102 Y A 0.0000
103 S A -1.3237
104 N A -1.9608
105 V A 0.0000
106 T A -0.2148
107 A A -0.4276
108 T A -0.3182
109 R A -1.4511
110 L A -0.2530
111 L A 0.0000
112 S A -0.5713
113 S A 0.0000
114 T A -0.2264
115 N A -0.2354
116 S A -0.1952
117 R A 0.0000
118 L A -0.2203
119 C A 0.0000
120 A A 0.0000
121 V A 0.0000
122 F A 0.0000
123 V A 0.2401
124 R A -0.6509
125 S A -0.7703
126 G A -0.9944
127 Q A -0.8489
128 P A -0.3455
129 V A 0.3189
130 I A 0.0000
131 G A 0.0000
132 A A 0.0000
133 C A 0.0000
134 T A 0.0000
135 S A -0.0894
136 P A -0.1146
137 Y A 0.1932
138 D A -1.5053
139 G A -1.0033
140 K A -1.0148
141 Y A 0.5022
142 V A 0.5433
143 S A -0.3885
144 K A -0.8740
145 Y A -0.4681
146 E A -1.6601
147 E A -1.8664
148 L A 0.0000
149 K A -2.1490
150 K A -2.7710
151 K A 0.0000
152 L A 0.0000
153 E A -2.4429
154 E A -1.7039
155 V A 0.0000
156 A A -0.9275 mutated: YA156A
157 A A -0.6156 mutated: VA157A
158 A A -0.1314
159 G A -0.0972
160 I A 0.4631
161 A A -0.2721 mutated: SA161A
162 V A 0.0000
163 R A -1.6273
164 V A 0.0000
165 H A 0.0000
166 V A 0.0000
167 S A -0.6913
168 K A 0.0000
169 E A -3.0274
170 E A -2.8761
171 Q A 0.0000
172 Y A 0.0000
173 Y A 0.0000
174 D A 0.0000
175 Y A 0.0000
176 E A -1.7641
177 D A -1.9729
178 A A -0.5378
179 T A -0.2276
180 F A 0.0000
181 E A -0.7480
182 T A 0.0000
183 Y A 0.0000
184 A A -0.3725
185 L A 0.0000
186 T A -0.0254
187 G A 0.0000
188 I A 0.0000
189 S A -0.5780
190 I A 0.0000
191 C A 0.0618
192 N A -0.6046
193 P A -0.5797
194 G A -0.6373
195 S A -0.4708
196 S A -0.3022
197 L A 0.1546
198 C A 0.6595
Download PDB file
View in 3Dmol

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, -0.5854 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_8 -0.5854 View CSV PDB
model_1 -0.6674 View CSV PDB
model_0 -0.6762 View CSV PDB
model_3 -0.6809 View CSV PDB
model_6 -0.684 View CSV PDB
model_2 -0.6946 View CSV PDB
input -0.721 View CSV PDB
model_11 -0.7428 View CSV PDB
CABS_average -0.744 View CSV PDB
model_10 -0.8042 View CSV PDB
model_5 -0.8225 View CSV PDB
model_9 -0.8299 View CSV PDB
model_4 -0.8433 View CSV PDB
model_7 -0.8964 View CSV PDB