Project name: PrP 1QLX

Status: done

Started: 2026-04-17 00:50:40
Chain sequence(s) A: LGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQR
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]                                                (00:00:12)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:12)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:12)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:12)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:13)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:50)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:13:34)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:13:35)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:13:35)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:13:35)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:13:36)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:13:36)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:13:36)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:13:37)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:13:37)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:13:37)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:13:38)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:13:38)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:13:38)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:13:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:13:43)
Show buried residues
Minimal score value
-2.9138
Maximal score value
1.9075
Average score
-0.7457
Total score value
-77.5559
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
125 L A 1.4952
126 G A 0.3771
127 G A 0.7995
128 Y A 1.9075
129 M A 1.6050
130 L A 1.5549
131 G A 0.0000
132 S A 0.3287
133 A A 0.1995
134 M A 0.5596
135 S A -0.7538
136 R A -1.5379
137 P A -0.4987
138 I A 0.0412
139 I A 0.0000
140 H A -1.4151
141 F A -0.1553
142 G A -0.4877
143 S A -1.0096
144 D A -1.6961
145 Y A -0.5536
146 E A -1.0503
147 D A 0.0000
148 R A -2.5562
149 Y A -0.7832
150 Y A -1.9648
151 R A -2.8604
152 E A -2.9138
153 N A -2.3915
154 M A -1.1237
155 H A -1.7298
156 R A -1.3498
157 Y A -0.6141
158 P A -0.7537
159 N A -0.6874
160 Q A -0.5047
161 V A 0.0000
162 Y A 1.0528
163 Y A 0.0000
164 R A 0.7228
165 P A 0.0000
166 M A -0.3644
167 D A -1.1256
168 E A -1.8070
169 Y A 0.0000
170 S A -1.6603
171 N A -2.0510
172 Q A -2.4161
173 N A -2.7698
174 N A -2.5744
175 F A -1.5076
176 V A -1.6294
177 H A -2.2561
178 D A -1.5233
179 C A 0.0000
180 V A 0.0000
181 N A -1.3455
182 I A -0.8413
183 T A 0.0000
184 I A 0.0000
185 K A -1.3331
186 Q A -0.8392
187 H A 0.0000
188 T A -0.4964
189 V A 0.6066
190 T A -0.3304
191 T A 0.0000
192 T A -0.8257
193 T A -0.8815
194 K A -2.0487
195 G A -1.5773
196 E A -1.6370
197 N A -1.6016
198 F A -0.7823
199 T A -1.2927
200 E A -1.9718
201 T A -1.2924
202 D A 0.0000
203 V A -1.1156
204 K A -1.6476
205 M A 0.0000
206 M A 0.0000
207 E A -1.3508
208 R A -0.8703
209 V A 0.0000
210 V A 0.0000
211 E A -0.7435
212 Q A 0.0000
213 M A 0.0000
214 C A 0.0000
215 I A -0.8636
216 T A 0.0000
217 Q A 0.0000
218 Y A -1.2554
219 E A -1.8806
220 R A -1.6973
221 E A 0.0000
222 S A -1.3918
223 Q A -1.7137
224 A A -1.0987
225 Y A -0.1149
226 Y A 0.1351
227 Q A -1.3275
228 R A -1.6970
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, -0.7457 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_6 -0.7457 View CSV PDB
model_0 -0.7739 View CSV PDB
model_7 -0.8013 View CSV PDB
model_3 -0.8365 View CSV PDB
model_11 -0.8608 View CSV PDB
CABS_average -0.9054 View CSV PDB
model_9 -0.9163 View CSV PDB
model_5 -0.9639 View CSV PDB
model_1 -0.9653 View CSV PDB
model_10 -0.9748 View CSV PDB
model_4 -1.0007 View CSV PDB
model_8 -1.0081 View CSV PDB
model_2 -1.0173 View CSV PDB
input -1.0671 View CSV PDB