Project name: PTx S2 V1

Status: done

Started: 2025-04-25 15:38:38
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]                                                (00:00:00)
[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]       CABS:     Running CABS flex simulation                                                (00:01:28)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:23:37)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:23:38)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:23:38)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:23:39)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:23:39)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:23:40)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:23:41)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:23:41)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:23:42)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:23:43)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:23:43)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:23:44)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:23:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:23:47)
[INFO]       Main:     Simulation completed successfully.                                          (00:23:48)
Show buried residues
Minimal score value
-3.8737
Maximal score value
2.1629
Average score
-0.5811
Total score value
-115.0625
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 -0.2759
2 P A -0.4007
3 G A -0.3282
4 I A 0.3236
5 V A 0.0550
6 I A 0.0000
7 P A 0.0000
8 P A -1.9401
9 Q A -1.6374
10 E A -2.3458
11 Q A -1.8266
12 I A -0.8425
13 T A -1.0618
14 Q A -0.9456
15 H A -1.0924
16 G A -0.7830
17 S A -0.3300
18 P A 0.0929
19 Y A 0.6167
20 G A -0.6172
21 R A -1.4601
22 C A -0.5156
23 A A -0.9806
24 N A -1.8068
25 K A -1.5214
26 T A -0.8489
27 R A 0.0000
28 A A -0.0946
29 L A 0.0000
30 T A -0.2759
31 V A 0.0000
32 A A -1.3342
33 E A -1.4008
34 L A 0.0000
35 R A -2.3565
36 G A -1.8388
37 S A -1.9715
38 G A -2.2232
39 D A -3.1519
40 L A 0.0000
41 Q A 0.0000
42 E A -3.5837
43 Y A -2.3111
44 L A 0.0000
45 R A -3.4695
46 H A -2.3792
47 V A -0.9683
48 T A -0.7028
49 R A -0.8841
50 G A 0.0028
51 W A 0.9425
52 S A 1.3670
53 I A 2.1288
54 F A 0.0000
55 A A 0.0000
56 L A 0.0000
57 Y A 0.4422
58 D A -1.7983
59 G A 0.0000
60 T A 0.0000
61 Y A 0.0000
62 L A 0.9725
63 G A 0.1384
64 G A -1.2647
65 E A -2.5905
66 Y A -1.4366
67 G A -1.0690
68 G A -0.7865
69 V A -0.2635
70 I A -0.8212
71 K A -2.2780
72 D A -2.9572
73 G A -2.3207
74 T A -1.7573
75 P A -1.0344
76 G A -0.9378
77 G A -0.3479
78 A A 0.0943
79 F A 1.3474
80 D A -0.1150
81 L A 1.1034
82 K A 0.7253
83 T A 0.4188
84 T A 0.0000
85 F A 0.0000
86 C A 0.0000
87 I A 0.0000
88 M A -0.9728
89 T A 0.0000
90 T A -1.4730
91 R A -2.6984
92 N A -2.7273
93 T A -1.9247
94 G A -1.4226
95 Q A -1.4871
96 P A -1.0287
97 A A -0.9651
98 T A -1.5461
99 D A -2.2294
100 H A -0.8328
101 Y A 0.0562
102 Y A 0.0000
103 S A 0.0000
104 N A -0.6205
105 V A 0.0000
106 T A 0.3639
107 A A 0.3817
108 T A 0.1508
109 R A -0.7180
110 L A 0.3843
111 L A 0.3825
112 S A -0.0187
113 S A 0.0000
114 T A -0.5957
115 N A -0.8954
116 S A -0.6223
117 R A 0.0000
118 L A -0.2035
119 C A 0.0000
120 A A 0.0000
121 V A 0.0000
122 F A 0.0000
123 V A 0.2469
124 R A 0.0000
125 S A -0.4329
126 G A -0.6150
127 Q A -0.3420
128 P A -0.0224
129 V A 0.6943
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 0.0000
136 P A -0.2165
137 Y A 0.0649
138 D A -1.3996
139 G A -1.2769
140 K A -1.2666
141 Y A -0.6523
142 V A 0.1951
143 S A -0.8635
144 K A -1.7776
145 Y A -1.2514
146 E A -2.9197
147 E A -3.2824
148 L A 0.0000
149 K A -2.9737
150 K A -3.8737
151 K A -2.6603
152 L A 0.0000
153 E A -1.7428
154 E A -1.9177
155 V A 0.0000
156 Y A 0.6523
157 V A 1.4221
158 A A 0.8115
159 G A 1.0349
160 I A 2.1629
161 S A 1.0289
162 V A 0.0000
163 R A -0.1993
164 V A 0.0000
165 H A -0.7601
166 V A 0.0000
167 S A -1.1637
168 K A -1.7610
169 E A -1.9690
170 E A -1.6354
171 Q A 0.0000
172 Y A 0.0000
173 Y A -0.5445
174 D A -0.2969
175 Y A -0.1850
176 E A -1.3139
177 D A -1.8818
178 A A -1.1181
179 T A -0.7035
180 F A -0.3612
181 E A -0.8658
182 T A 0.0000
183 Y A 0.0000
184 A A 0.0000
185 L A 0.0000
186 T A -0.4615
187 G A -0.4393
188 I A 0.0000
189 S A 0.7113
190 I A 1.9866
191 C A 1.0417
192 N A -0.6726
193 P A -0.6619
194 G A -0.8637
195 S A -0.5153
196 S A 0.2538
197 L A 1.6578
198 C A 1.6094
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, -0.5811 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 -0.5811 View CSV PDB
model_9 -0.6333 View CSV PDB
input -0.6713 View CSV PDB
model_1 -0.6737 View CSV PDB
model_4 -0.683 View CSV PDB
model_11 -0.6878 View CSV PDB
model_5 -0.6977 View CSV PDB
model_6 -0.7035 View CSV PDB
CABS_average -0.7089 View CSV PDB
model_2 -0.7161 View CSV PDB
model_7 -0.743 View CSV PDB
model_3 -0.7609 View CSV PDB
model_0 -0.776 View CSV PDB
model_10 -0.8509 View CSV PDB