Project name: PTx S2 V1

Status: done

Started: 2025-04-25 15:33:12
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
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]       CABS:     Running CABS flex simulation                                                (00:01:20)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:23:25)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:23:26)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:23:26)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:23:27)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:23:28)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:23:28)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:23:29)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:23:29)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:23:30)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:23:31)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:23:31)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:23:32)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:23:33)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:23:35)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:36)
Show buried residues
Minimal score value
-3.3656
Maximal score value
1.5016
Average score
-0.5742
Total score value
-113.6924
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 -0.3159
2 P A -0.3948
3 G A -0.5341
4 I A 0.0000
5 V A 0.5888
6 I A 0.0000
7 P A -0.4457
8 P A -1.1879
9 Q A -1.5331
10 E A -1.2765
11 Q A -1.0994
12 I A 0.2940
13 T A -0.3647
14 Q A -0.6083
15 H A -0.9623
16 G A 0.0000
17 S A -0.6021
18 P A -0.3723
19 Y A -0.1007
20 G A -0.8665
21 R A -1.2300
22 C A -0.3198
23 A A -0.7321
24 N A -1.2756
25 K A -1.2094
26 T A -0.5988
27 R A 0.0000
28 A A 0.3039
29 L A 0.0000
30 T A -0.3890
31 V A -1.2722
32 A A -1.2615
33 E A -1.6631
34 L A 0.0000
35 R A -2.6435
36 G A -2.0430
37 S A -2.0375
38 G A -2.0339
39 D A -2.4800
40 L A 0.0000
41 Q A -2.3248
42 E A -2.7587
43 Y A -1.1404
44 L A 0.0000
45 R A -2.8956
46 H A -2.1378
47 V A -0.8358
48 T A -0.6043
49 R A -0.8502
50 G A 0.0184
51 W A 0.8998
52 S A 0.2788
53 I A 0.0000
54 F A 0.0000
55 A A 0.0000
56 L A 0.0000
57 Y A 0.8509
58 D A -0.9039
59 G A 0.0000
60 T A -0.6286
61 Y A 0.0000
62 L A -0.0250
63 G A 0.0000
64 G A -1.4399
65 E A -1.6015
66 Y A 0.0549
67 G A -0.4949
68 G A -0.7906
69 V A 0.1784
70 I A -0.5560
71 K A -2.4449
72 D A -2.6703
73 G A -1.8797
74 T A -1.0052
75 P A -0.5695
76 G A -0.5183
77 G A -0.5700
78 A A 0.0000
79 F A 1.0044
80 D A -0.6576
81 L A 0.7174
82 K A 0.0016
83 T A 0.0000
84 T A 0.1614
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 -1.9840
91 R A -3.1842
92 N A -3.3248
93 T A -2.3900
94 G A -1.8244
95 Q A -2.1316
96 P A -1.2911
97 A A -1.0631
98 T A -1.5256
99 D A -1.3097
100 H A -0.2940
101 Y A 0.7495
102 Y A -0.1038
103 S A -0.5526
104 N A -1.6031
105 V A 0.0000
106 T A -0.5294
107 A A 0.0000
108 T A -0.2215
109 R A -1.4747
110 L A -0.0474
111 L A 0.0000
112 S A -0.1406
113 S A 0.0000
114 T A -0.1537
115 N A -0.5007
116 S A -0.2645
117 R A 0.0000
118 L A 0.1148
119 C A 0.0000
120 A A 0.0000
121 V A 0.0000
122 F A 0.0000
123 V A -1.2767
124 R A -2.4445
125 S A -1.6505
126 G A -1.2712
127 Q A -1.1197
128 P A -0.7491
129 V A 0.1139
130 I A 0.0000
131 G A 0.0473
132 A A 0.0000
133 C A 0.0000
134 T A 0.0000
135 S A -0.3706
136 P A 0.0000
137 Y A -0.1150
138 D A -1.1291
139 G A -0.7316
140 K A -1.0046
141 Y A 0.4384
142 V A 0.7626
143 S A -0.3151
144 K A -1.2919
145 Y A 0.0000
146 E A -2.0984
147 E A -3.2416
148 L A 0.0000
149 K A -2.6938
150 K A -3.3656
151 K A -1.9573
152 L A 0.0000
153 E A -1.2359
154 E A -1.1703
155 V A 0.0000
156 Y A 0.6085
157 V A 1.4634
158 A A 1.1166
159 G A 0.4409
160 I A 1.2845
161 S A 0.1875
162 V A 0.0000
163 R A 0.0650
164 V A 0.0000
165 H A 0.0000
166 V A 0.0000
167 S A -1.2823
168 K A -2.5157
169 E A -3.1896
170 E A -3.1620
171 Q A -2.3835
172 Y A 0.0000
173 Y A 0.0326
174 D A 0.0000
175 Y A 0.2572
176 E A -0.7503
177 D A -0.4370
178 A A 0.1138
179 T A 0.6417
180 F A 1.5016
181 E A 0.0027
182 T A 0.0000
183 Y A 0.0000
184 A A -0.8314
185 L A 0.0000
186 T A -0.0490
187 G A 0.0000
188 I A 0.0000
189 S A 0.0000
190 I A 1.5009
191 C A 0.9442
192 N A -0.1716
193 P A -0.4272
194 G A -0.2266
195 S A -0.0517
196 S A 0.1857
197 L A 0.4429
198 C A 0.7208
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, -0.5742 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_9 -0.5742 View CSV PDB
model_7 -0.5841 View CSV PDB
model_10 -0.6198 View CSV PDB
model_8 -0.6242 View CSV PDB
model_1 -0.6512 View CSV PDB
model_3 -0.655 View CSV PDB
model_11 -0.6569 View CSV PDB
input -0.6713 View CSV PDB
CABS_average -0.6801 View CSV PDB
model_5 -0.7221 View CSV PDB
model_4 -0.7234 View CSV PDB
model_0 -0.7296 View CSV PDB
model_6 -0.7582 View CSV PDB
model_2 -0.8626 View CSV PDB