Project name: full? PrP wild type

Status: done

Started: 2026-03-26 19:28:28
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]                                                (00:00:00)
[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                                                (00:01:37)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:12:20)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:12:20)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:12:21)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:12:21)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:12:21)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:12:21)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:12:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:26)
Show buried residues
Minimal score value
-3.0014
Maximal score value
1.5609
Average score
-0.8008
Total score value
-83.2816
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 1.5609
126 G A 0.8380
127 G A 0.6865
128 Y A 1.3327
129 M A 1.2095
130 L A 1.5344
131 G A 0.6315
132 S A -0.0238
133 A A -0.4287
134 M A -0.8962
135 S A -1.0324
136 R A -1.9934
137 P A -0.9221
138 I A 0.0000
139 I A 0.0000
140 H A -0.7634
141 F A 1.1887
142 G A 0.2409
143 S A -0.3813
144 D A -0.7621
145 Y A -0.0080
146 E A -0.8701
147 D A 0.0000
148 R A -2.0104
149 Y A -0.7436
150 Y A 0.0000
151 R A -1.9973
152 E A -2.0308
153 N A -2.1033
154 M A 0.0000
155 H A -2.3950
156 R A -2.9032
157 Y A 0.0000
158 P A -1.3728
159 N A -0.8825
160 Q A 0.3377
161 V A 0.0000
162 Y A 0.0000
163 Y A 0.0000
164 R A -1.2082
165 P A -0.5431
166 M A -0.4646
167 D A -2.0003
168 E A -2.2869
169 Y A 0.0000
170 S A -1.9872
171 N A -2.5825
172 Q A -2.9139
173 N A -2.8140
174 N A -2.6011
175 F A -2.0945
176 V A 0.0000
177 H A -2.0047
178 D A -1.8985
179 C A 0.0000
180 V A 0.0000
181 N A -1.2866
182 I A -0.5419
183 T A 0.0000
184 I A 0.0000
185 K A -0.9445
186 Q A 0.0000
187 H A 0.0000
188 T A -0.1997
189 V A 1.0107
190 T A 0.1390
191 T A 0.0000
192 T A -1.0247
193 T A -0.7169
194 K A -2.4389
195 G A -2.1969
196 E A -3.0014
197 N A -2.4497
198 F A -1.1888
199 T A -1.1169
200 E A -1.9410
201 T A -1.1299
202 D A -1.0001
203 V A -0.8497
204 K A -1.3269
205 M A 0.0000
206 M A 0.0000
207 E A -1.3430
208 R A -1.2314
209 V A 0.0000
210 V A 0.0000
211 E A -1.2762
212 Q A -0.3407
213 M A 0.0000
214 C A 0.0000
215 I A -0.7607
216 T A -0.9335
217 Q A 0.0000
218 Y A 0.0000
219 E A -2.4915
220 R A -2.6543
221 E A -1.9678
222 S A -1.4061
223 Q A -1.9094
224 A A -1.3210
225 Y A -0.0631
226 Y A 0.2255
227 Q A -1.3359
228 R A -1.9086
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, -0.8008 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_0 -0.8008 View CSV PDB
model_1 -0.8397 View CSV PDB
model_4 -0.8865 View CSV PDB
model_5 -0.8919 View CSV PDB
model_6 -0.8973 View CSV PDB
model_10 -0.9006 View CSV PDB
CABS_average -0.9205 View CSV PDB
model_9 -0.9232 View CSV PDB
model_11 -0.9475 View CSV PDB
model_3 -0.9477 View CSV PDB
model_8 -0.9642 View CSV PDB
model_2 -0.9708 View CSV PDB
input -1.0671 View CSV PDB
model_7 -1.076 View CSV PDB