Project name: Rhodopsin
Status: done
Started: 2025-03-14 13:27:11
| Chain sequence(s) |
A: MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 5 Å |
| FoldX usage | Yes |
| pH calculations | No |
| alphaCutter usage | Used: no changes made |
| 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] PDB: Running AlphaCutter (00:00:01)
[INFO] PDB: AlphaCutter did not cut any residues. The original structure will be used
for analysis. (00:00:07)
[INFO] FoldX: Starting FoldX energy minimization (00:00:07)
[INFO] CABS: Running CABS flex simulation (00:04:15)
[INFO] Analysis: Starting Aggrescan4D on model_8.pdb (00:50:31)
[INFO] Analysis: Starting Aggrescan4D on model_6.pdb (00:50:32)
[INFO] Analysis: Starting Aggrescan4D on model_11.pdb (00:50:34)
[INFO] Analysis: Starting Aggrescan4D on model_7.pdb (00:50:35)
[INFO] Analysis: Starting Aggrescan4D on model_3.pdb (00:50:37)
[INFO] Analysis: Starting Aggrescan4D on model_5.pdb (00:50:38)
[INFO] Analysis: Starting Aggrescan4D on model_1.pdb (00:50:40)
[INFO] Analysis: Starting Aggrescan4D on model_0.pdb (00:50:41)
[INFO] Analysis: Starting Aggrescan4D on model_2.pdb (00:50:43)
[INFO] Analysis: Starting Aggrescan4D on model_4.pdb (00:50:44)
[INFO] Analysis: Starting Aggrescan4D on model_10.pdb (00:50:45)
[INFO] Analysis: Starting Aggrescan4D on model_9.pdb (00:50:47)
[INFO] Analysis: Starting Aggrescan4D on input.pdb (00:50:48)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:50:55)
[INFO] Main: Simulation completed successfully. (00:50:57)
|
Note Your prediction results will be deleted after 360 days.
Drag cursor over the plot to display residue labels.
Show buried residues
- Minimal score value
- -2.4565
- Maximal score value
- 2.3832
- Average score
- 0.1049
- Total score value
- 36.5118
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 | M | A | 0.8686 | |
| 2 | N | A | -0.9127 | |
| 3 | G | A | -0.2804 | |
| 4 | T | A | -0.3719 | |
| 5 | E | A | -1.8661 | |
| 6 | G | A | -0.7198 | |
| 7 | P | A | -0.2346 | |
| 8 | N | A | -0.5588 | |
| 9 | F | A | 0.0000 | |
| 10 | Y | A | -0.1628 | |
| 11 | V | A | 0.0000 | |
| 12 | P | A | 0.0000 | |
| 13 | F | A | 0.7176 | |
| 14 | S | A | 0.0000 | |
| 15 | N | A | -1.4153 | |
| 16 | A | A | -0.1855 | |
| 17 | T | A | -0.1043 | |
| 18 | G | A | -0.5378 | |
| 19 | V | A | 0.5538 | |
| 20 | V | A | 1.1178 | |
| 21 | R | A | 0.0000 | |
| 22 | S | A | 0.0000 | |
| 23 | P | A | 0.0000 | |
| 24 | F | A | -0.0294 | |
| 25 | E | A | -1.6047 | |
| 26 | Y | A | 0.3982 | |
| 27 | P | A | -0.3249 | |
| 28 | Q | A | -1.2011 | |
| 29 | Y | A | 0.2528 | |
| 30 | Y | A | 1.3911 | |
| 31 | L | A | 0.4099 | |
| 32 | A | A | -0.3376 | |
| 33 | E | A | -1.7452 | |
| 34 | P | A | -0.5157 | |
| 35 | W | A | 0.8889 | |
| 36 | Q | A | 0.2777 | |
| 37 | F | A | 0.5144 | |
| 38 | S | A | 0.2935 | |
| 39 | M | A | 0.6905 | |
| 40 | L | A | 0.0000 | |
| 41 | A | A | 0.0364 | |
| 42 | A | A | 0.5004 | |
| 43 | Y | A | 1.0935 | |
| 44 | M | A | 0.0000 | |
| 45 | F | A | 2.2296 | |
| 46 | L | A | 1.9985 | |
| 47 | L | A | 0.5092 | |
| 48 | I | A | 0.4891 | |
| 49 | V | A | 1.1034 | |
| 50 | L | A | 0.6244 | |
| 51 | G | A | 0.0000 | |
| 52 | F | A | 1.1319 | |
| 53 | P | A | 0.2482 | |
| 54 | I | A | 0.1611 | |
| 55 | N | A | 0.0000 | |
| 56 | F | A | 1.6901 | |
| 57 | L | A | 0.0000 | |
| 58 | T | A | 0.0000 | |
| 59 | L | A | 0.5829 | |
| 60 | Y | A | 0.9723 | |
| 61 | V | A | 0.0000 | |
| 62 | T | A | 0.0000 | |
| 63 | V | A | 0.8089 | |
| 64 | Q | A | -1.1935 | |
| 65 | H | A | -1.4201 | |
| 66 | K | A | -2.2049 | |
| 67 | K | A | -2.0166 | |
| 68 | L | A | 0.0000 | |
| 69 | R | A | -1.1478 | |
| 70 | T | A | 0.0000 | |
| 71 | P | A | 0.0000 | |
| 72 | L | A | 0.0000 | |
| 73 | N | A | 0.0000 | |
| 74 | Y | A | 0.2589 | |
| 75 | I | A | 0.0000 | |
| 76 | L | A | 0.0000 | |
| 77 | L | A | 0.0000 | |
| 78 | N | A | -0.2107 | |
| 79 | L | A | 0.0000 | |
| 80 | A | A | 0.0000 | |
| 81 | V | A | 0.5715 | |
| 82 | A | A | 0.0000 | |
| 83 | D | A | 0.0000 | |
| 84 | L | A | 0.7016 | |
| 85 | F | A | 1.2922 | |
| 86 | M | A | 0.0000 | |
| 87 | V | A | 0.0000 | |
| 88 | L | A | 1.6350 | |
| 89 | G | A | 0.1824 | |
| 90 | G | A | 0.0000 | |
| 91 | F | A | 0.0000 | |
| 92 | T | A | -0.0375 | |
| 93 | S | A | -0.0558 | |
| 94 | T | A | 0.0000 | |
| 95 | L | A | 0.4211 | |
| 96 | Y | A | 1.3477 | |
| 97 | T | A | 0.0000 | |
| 98 | S | A | 0.0000 | |
| 99 | L | A | 0.8109 | |
| 100 | H | A | -0.8199 | |
| 101 | G | A | -0.3248 | |
| 102 | Y | A | 0.0000 | |
| 103 | F | A | 1.1129 | |
| 104 | V | A | 1.9683 | |
| 105 | F | A | 0.5715 | |
| 106 | G | A | -0.1436 | |
| 107 | P | A | -0.3029 | |
| 108 | T | A | -0.1617 | |
| 109 | G | A | -0.2373 | |
| 110 | C | A | 0.0000 | |
| 111 | N | A | 0.1156 | |
| 112 | L | A | 1.5409 | |
| 113 | E | A | 0.0925 | |
| 114 | G | A | 0.0000 | |
| 115 | F | A | 0.6877 | |
| 116 | F | A | 0.0000 | |
| 117 | A | A | 0.0135 | |
| 118 | T | A | 0.0000 | |
| 119 | L | A | 0.0000 | |
| 120 | G | A | 0.0000 | |
| 121 | G | A | -0.0487 | |
| 122 | E | A | 0.0000 | |
| 123 | I | A | 0.0000 | |
| 124 | A | A | 0.0007 | |
| 125 | L | A | 0.0000 | |
| 126 | W | A | 0.1387 | |
| 127 | S | A | 0.0000 | |
| 128 | L | A | 0.0000 | |
| 129 | V | A | 0.0000 | |
| 130 | V | A | 0.0000 | |
| 131 | L | A | 0.0000 | |
| 132 | A | A | 0.0000 | |
| 133 | I | A | 1.1829 | |
| 134 | E | A | 0.0000 | |
| 135 | R | A | 0.0000 | |
| 136 | Y | A | 0.6843 | |
| 137 | V | A | 0.4938 | |
| 138 | V | A | 0.0000 | |
| 139 | V | A | 0.0000 | |
| 140 | C | A | 0.5049 | |
| 141 | K | A | -0.8038 | |
| 142 | P | A | -0.1130 | |
| 143 | M | A | 0.9981 | |
| 144 | S | A | 0.1584 | |
| 145 | N | A | -0.0335 | |
| 146 | F | A | 1.7516 | |
| 147 | R | A | -0.2796 | |
| 148 | F | A | 0.0000 | |
| 149 | G | A | -0.2072 | |
| 150 | E | A | -0.7683 | |
| 151 | N | A | -1.4089 | |
| 152 | H | A | -1.0013 | |
| 153 | A | A | 0.0000 | |
| 154 | I | A | 0.6412 | |
| 155 | M | A | 1.1605 | |
| 156 | G | A | 0.3691 | |
| 157 | V | A | 0.0000 | |
| 158 | A | A | 0.3922 | |
| 159 | F | A | 2.1327 | |
| 160 | T | A | 0.0000 | |
| 161 | W | A | 0.9613 | |
| 162 | V | A | 2.1458 | |
| 163 | M | A | 0.5807 | |
| 164 | A | A | 0.0000 | |
| 165 | L | A | 1.2200 | |
| 166 | A | A | 0.3067 | |
| 167 | C | A | 0.0000 | |
| 168 | A | A | 0.0000 | |
| 169 | A | A | 0.0090 | |
| 170 | P | A | -0.0605 | |
| 171 | P | A | 0.0000 | |
| 172 | L | A | 1.5588 | |
| 173 | A | A | 0.2743 | |
| 174 | G | A | -0.1354 | |
| 175 | W | A | 1.0829 | |
| 176 | S | A | 0.0000 | |
| 177 | R | A | -0.0914 | |
| 178 | Y | A | 0.0899 | |
| 179 | I | A | 0.0000 | |
| 180 | P | A | 0.0000 | |
| 181 | E | A | 0.0000 | |
| 182 | G | A | 0.0000 | |
| 183 | L | A | 0.0000 | |
| 184 | Q | A | 0.0000 | |
| 185 | C | A | 0.0787 | |
| 186 | S | A | 0.0000 | |
| 187 | C | A | 0.0000 | |
| 188 | G | A | 0.0000 | |
| 189 | I | A | 0.0000 | |
| 190 | D | A | 0.0000 | |
| 191 | Y | A | 0.0000 | |
| 192 | Y | A | 0.0000 | |
| 193 | T | A | 0.0000 | |
| 194 | L | A | 0.0000 | |
| 195 | K | A | -0.6258 | |
| 196 | P | A | -0.6690 | |
| 197 | E | A | -1.7834 | |
| 198 | V | A | 0.0849 | |
| 199 | N | A | -1.1451 | |
| 200 | N | A | 0.0000 | |
| 201 | E | A | -0.2558 | |
| 202 | S | A | -0.1284 | |
| 203 | F | A | 0.6456 | |
| 204 | V | A | 0.0000 | |
| 205 | I | A | 0.8672 | |
| 206 | Y | A | 1.5354 | |
| 207 | M | A | 0.0000 | |
| 208 | F | A | 0.0000 | |
| 209 | V | A | 1.0318 | |
| 210 | V | A | 0.5061 | |
| 211 | H | A | 0.0000 | |
| 212 | F | A | 0.3740 | |
| 213 | T | A | 0.2552 | |
| 214 | I | A | 0.6337 | |
| 215 | P | A | 0.0000 | |
| 216 | M | A | 0.4642 | |
| 217 | I | A | 2.0943 | |
| 218 | I | A | 1.6890 | |
| 219 | I | A | 0.0000 | |
| 220 | F | A | 2.2907 | |
| 221 | F | A | 2.2108 | |
| 222 | C | A | 0.0000 | |
| 223 | Y | A | 0.0841 | |
| 224 | G | A | -0.6021 | |
| 225 | Q | A | -1.2754 | |
| 226 | L | A | 0.0000 | |
| 227 | V | A | 1.2981 | |
| 228 | F | A | 1.9327 | |
| 229 | T | A | 0.2030 | |
| 230 | V | A | 0.0000 | |
| 231 | K | A | -1.7436 | |
| 232 | E | A | -1.6705 | |
| 233 | A | A | 0.0000 | |
| 234 | A | A | -0.1567 | |
| 235 | A | A | -0.0164 | |
| 236 | Q | A | -0.5207 | |
| 237 | Q | A | -0.7500 | |
| 238 | Q | A | 0.0000 | |
| 239 | E | A | -1.8502 | |
| 240 | S | A | -0.5015 | |
| 241 | A | A | 0.0067 | |
| 242 | T | A | -0.2232 | |
| 243 | T | A | 0.0000 | |
| 244 | Q | A | 0.0000 | |
| 245 | K | A | -1.7823 | |
| 246 | A | A | 0.0000 | |
| 247 | E | A | 0.0000 | |
| 248 | K | A | -0.9981 | |
| 249 | E | A | -0.6247 | |
| 250 | V | A | 0.0000 | |
| 251 | T | A | 0.0000 | |
| 252 | R | A | -1.8022 | |
| 253 | M | A | -0.1301 | |
| 254 | V | A | 0.0000 | |
| 255 | I | A | 0.3576 | |
| 256 | I | A | 0.9542 | |
| 257 | M | A | 0.0000 | |
| 258 | V | A | 0.0000 | |
| 259 | I | A | 1.9232 | |
| 260 | A | A | 0.0000 | |
| 261 | F | A | 0.0000 | |
| 262 | L | A | 1.1762 | |
| 263 | I | A | 2.1624 | |
| 264 | C | A | 0.0000 | |
| 265 | W | A | 0.2173 | |
| 266 | V | A | 0.3384 | |
| 267 | P | A | 0.0192 | |
| 268 | Y | A | 0.0000 | |
| 269 | A | A | 0.0037 | |
| 270 | S | A | -0.1927 | |
| 271 | V | A | 0.0000 | |
| 272 | A | A | 0.0000 | |
| 273 | F | A | 2.0664 | |
| 274 | Y | A | 1.6462 | |
| 275 | I | A | 0.0000 | |
| 276 | F | A | 0.5635 | |
| 277 | T | A | 0.1384 | |
| 278 | H | A | -0.4624 | |
| 279 | Q | A | -1.3303 | |
| 280 | G | A | -0.7116 | |
| 281 | S | A | -0.2148 | |
| 282 | N | A | -0.2358 | |
| 283 | F | A | 0.0000 | |
| 284 | G | A | -0.2214 | |
| 285 | P | A | 0.0000 | |
| 286 | I | A | 2.3832 | |
| 287 | F | A | 2.3253 | |
| 288 | M | A | 0.0000 | |
| 289 | T | A | 0.0000 | |
| 290 | I | A | 1.1977 | |
| 291 | P | A | 0.3343 | |
| 292 | A | A | 0.0000 | |
| 293 | F | A | 0.0000 | |
| 294 | F | A | 0.6580 | |
| 295 | A | A | 0.0000 | |
| 296 | K | A | 0.0000 | |
| 297 | S | A | 0.0230 | |
| 298 | A | A | -0.0018 | |
| 299 | A | A | 0.0000 | |
| 300 | I | A | 0.5671 | |
| 301 | Y | A | 1.0658 | |
| 302 | N | A | 0.0000 | |
| 303 | P | A | 0.0000 | |
| 304 | V | A | 0.2083 | |
| 305 | I | A | 0.0000 | |
| 306 | Y | A | 0.0000 | |
| 307 | I | A | 0.0000 | |
| 308 | M | A | 0.3546 | |
| 309 | M | A | 0.0000 | |
| 310 | N | A | 0.0000 | |
| 311 | K | A | 0.0000 | |
| 312 | Q | A | -0.1925 | |
| 313 | F | A | 0.0000 | |
| 314 | R | A | 0.0000 | |
| 315 | N | A | -0.3832 | |
| 316 | C | A | -0.0061 | |
| 317 | M | A | 0.0000 | |
| 318 | L | A | 1.5951 | |
| 319 | T | A | 0.2038 | |
| 320 | T | A | 0.3357 | |
| 321 | I | A | 2.3212 | |
| 322 | C | A | 1.1089 | |
| 323 | C | A | 0.0000 | |
| 324 | G | A | -0.5573 | |
| 325 | K | A | -0.8149 | |
| 326 | N | A | -1.3860 | |
| 327 | P | A | -0.2583 | |
| 328 | L | A | 0.6248 | |
| 329 | G | A | -0.5946 | |
| 330 | D | A | -2.1904 | |
| 331 | D | A | -2.4565 | |
| 332 | E | A | -2.1517 | |
| 333 | A | A | 0.0000 | |
| 334 | S | A | 0.0000 | |
| 335 | A | A | 0.0497 | |
| 336 | T | A | -0.0360 | |
| 337 | V | A | 0.0000 | |
| 338 | S | A | 0.0000 | |
| 339 | K | A | 0.0000 | |
| 340 | T | A | 0.0000 | |
| 341 | E | A | 0.0000 | |
| 342 | T | A | 0.0000 | |
| 343 | S | A | -0.2526 | |
| 344 | Q | A | -1.2042 | |
| 345 | V | A | 0.0000 | |
| 346 | A | A | 0.0441 | |
| 347 | P | A | -0.0553 | |
| 348 | A | A | 0.0438 |
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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, 0.1049 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_4 | 0.1049 | View | CSV | PDB |
| model_0 | 0.1007 | View | CSV | PDB |
| model_2 | 0.0979 | View | CSV | PDB |
| model_9 | 0.0942 | View | CSV | PDB |
| model_10 | 0.0928 | View | CSV | PDB |
| model_5 | 0.0918 | View | CSV | PDB |
| model_7 | 0.0911 | View | CSV | PDB |
| CABS_average | 0.0877 | View | CSV | PDB |
| model_1 | 0.0857 | View | CSV | PDB |
| model_8 | 0.0829 | View | CSV | PDB |
| model_11 | 0.0764 | View | CSV | PDB |
| model_6 | 0.075 | View | CSV | PDB |
| model_3 | 0.0583 | View | CSV | PDB |
| input | 0.0212 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine