Project name: Human PrP dynamic

Status: done

Started: 2026-03-26 19:10:58
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)                                                   (00:00:01)
[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                                                (00:01:35)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:12:22)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:12:23)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:12:24)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:12:25)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:12:26)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:12:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:28)
Show buried residues
Minimal score value
-3.2296
Maximal score value
2.0021
Average score
-0.8638
Total score value
-89.8365
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 1.5002
126 G A 0.8869
127 G A 0.9851
128 Y A 2.0021
129 M A 1.6880
130 L A 1.3655
131 G A 0.5244
132 S A 0.1604
133 A A -0.0069
134 M A -0.1752
135 S A -0.8526
136 R A -1.8491
137 P A -1.3810
138 I A 0.0000
139 I A -1.6822
140 H A -2.2002
141 F A -1.6124
142 G A -1.3818
143 S A -1.3868
144 D A -1.9449
145 Y A -0.2753
146 E A -1.0290
147 D A 0.0000
148 R A -2.4516
149 Y A -0.8709
150 Y A 0.0000
151 R A -2.9925
152 E A -3.2296
153 N A 0.0000
154 M A 0.0000
155 H A -2.6507
156 R A -2.9952
157 Y A 0.0000
158 P A -0.8975
159 N A -0.7495
160 Q A 0.1424
161 V A 0.0000
162 Y A 0.7569
163 Y A 0.7634
164 R A -0.1684
165 P A -0.0632
166 M A -0.1709
167 D A -1.9783
168 E A -2.1799
169 Y A 0.0000
170 S A -1.8238
171 N A -2.3451
172 Q A -2.0664
173 N A -2.5231
174 N A -2.5164
175 F A -1.7146
176 V A 0.0000
177 H A -2.5412
178 D A -2.1828
179 C A 0.0000
180 V A 0.0000
181 N A -2.1282
182 I A -0.8251
183 T A 0.0000
184 I A -1.2236
185 K A -1.2912
186 Q A -0.4061
187 H A 0.0000
188 T A -0.3580
189 V A 0.5209
190 T A -0.2912
191 T A 0.0000
192 T A -0.8337
193 T A -0.7770
194 K A -2.0692
195 G A -1.8051
196 E A -1.9195
197 N A -2.2359
198 F A -1.3792
199 T A -1.2729
200 E A -2.2359
201 T A -1.5248
202 D A 0.0000
203 V A -1.6871
204 K A -2.3850
205 M A -1.7081
206 M A 0.0000
207 E A -2.2038
208 R A -2.2409
209 V A 0.0000
210 V A 0.0000
211 E A -2.1160
212 Q A -0.8105
213 M A 0.0000
214 C A 0.0000
215 I A -0.3796
216 T A -0.3881
217 Q A 0.0000
218 Y A -1.1581
219 E A -1.5921
220 R A -1.0543
221 E A 0.0000
222 S A -1.1459
223 Q A -1.4127
224 A A -0.8163
225 Y A 0.1330
226 Y A 0.3268
227 Q A -1.3432
228 R A -1.6852
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, -0.8638 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_1 -0.8638 View CSV PDB
model_11 -0.9112 View CSV PDB
model_9 -0.9117 View CSV PDB
model_3 -0.9305 View CSV PDB
model_7 -0.9494 View CSV PDB
model_2 -0.9496 View CSV PDB
model_4 -0.9636 View CSV PDB
CABS_average -0.9693 View CSV PDB
model_5 -0.9757 View CSV PDB
model_0 -1.0334 View CSV PDB
model_10 -1.0403 View CSV PDB
model_6 -1.0418 View CSV PDB
model_8 -1.0608 View CSV PDB
input -1.0671 View CSV PDB