| Chain sequence(s) |
A: GKVPTIVMVDAYKRYK
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| Dynamic mode | No |
| Automated mutations | Yes |
| 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 minimalization (00:00:00)
[INFO] Analysis: Starting Aggrescan3D on folded.pdb (00:00:08)
[INFO] Auto_mut: Residue number 7 from chain A and a score of 3.630 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 6 from chain A and a score of 3.014 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 8 from chain A and a score of 2.844 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 9 from chain A and a score of 1.784 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 5 from chain A and a score of 1.378 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 3 from chain A and a score of 0.699 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 4 from chain A and a score of 0.642 omitted from automated
muatation (excluded by the user). (00:00:08)
[INFO] Auto_mut: Residue number 11 from chain A and a score of -0.160 omitted from automated
muatation (excluded by the user). (00:00:08)
[CRITICAL] Auto_mut: Couldn't find residues suitable for automated mutations (exceeding a
threshold of -0.20). No automated mutations performed. (00:00:08)
[INFO] Main: Simulation completed successfully. (00:00:08)
|
The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan3D score | mutation |
|---|---|---|---|---|
| residue index | residue name | chain | Aggrescan3D score | |
| 1 | G | A | -0.9410 | |
| 2 | K | A | -1.1168 | |
| 3 | V | A | 0.6994 | |
| 4 | P | A | 0.6425 | |
| 5 | T | A | 1.3783 | |
| 6 | I | A | 3.0141 | |
| 7 | V | A | 3.6297 | |
| 8 | M | A | 2.8442 | |
| 9 | V | A | 1.7845 | |
| 10 | D | A | -0.4042 | |
| 11 | A | A | -0.1601 | |
| 12 | Y | A | -0.2349 | |
| 13 | K | A | -1.6794 | |
| 14 | R | A | -2.1119 | |
| 15 | Y | A | -0.7763 | |
| 16 | K | A | -1.4292 |
Automated mutations analysis
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated to glutamic acid, lysine, aspartic acid and arginine.
The table below shows 2 best scored mutants for each mutated residue. Protein variants
are ordered according to the mutation effect they had on protein stability
(energetic effect) together with the difference in the average per-residue aggregation score
between the wild type and the mutant (in the table green values indicate a positive change,
grey are neutral, and orange/red mean destabilizing or more aggregation prone mutants).
Summary for all the mutants can be found in this
CSV file.