| Chain sequence(s) |
A: AEGYQYRALYDYKKEREEDIDLHLGDILTVNKGSLVALGFSDGQEARPEEIGWLNGYNETTGERGDFPGTYVEYIGRKKISPP
input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | No |
| alphaCutter usage | No |
| 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 (00:00:47)
[INFO] Movie: Creting movie with webm format (00:00:47)
[CRITICAL] ffmpeg: OSError while launching ffmpeg. Perhaps it's not installed? (00:00:47)
[INFO] AutoMutEv:Residue number 40 from chain A and a score of 1.988 (leucine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Residue number 38 from chain A and a score of 1.622 (valine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Residue number 39 from chain A and a score of 1.292 (alanine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Residue number 26 from chain A and a score of 1.190 (leucine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Residue number 12 from chain A and a score of 1.113 (tyrosine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Residue number 41 from chain A and a score of 0.808 (glycine) selected for
automated mutation (00:00:48)
[INFO] AutoMutEv:Mutating residue number 40 from chain A (leucine) into methionine (00:00:48)
[INFO] AutoMutEv:Mutating residue number 38 from chain A (valine) into leucine (00:00:48)
[INFO] AutoMutEv:Mutating residue number 39 from chain A (alanine) into glycine (00:00:48)
[INFO] AutoMutEv:Mutating residue number 39 from chain A (alanine) into proline (00:01:10)
[INFO] AutoMutEv:Mutating residue number 38 from chain A (valine) into threonine (00:01:10)
[INFO] AutoMutEv:Mutating residue number 38 from chain A (valine) into methionine (00:01:12)
[INFO] AutoMutEv:Mutating residue number 39 from chain A (alanine) into serine (00:01:32)
[INFO] AutoMutEv:Mutating residue number 12 from chain A (tyrosine) into histidine (00:01:34)
[INFO] AutoMutEv:Mutating residue number 12 from chain A (tyrosine) into tryptophan (00:01:35)
[INFO] AutoMutEv:Mutating residue number 26 from chain A (leucine) into methionine (00:01:55)
[INFO] AutoMutEv:Mutating residue number 12 from chain A (tyrosine) into cysteine (00:02:00)
[INFO] AutoMutEv:Mutating residue number 41 from chain A (glycine) into aspartic acid (00:02:01)
[INFO] AutoMutEv:Mutating residue number 41 from chain A (glycine) into glutamic acid (00:02:19)
[INFO] AutoMutEv:Mutating residue number 41 from chain A (glycine) into asparagine (00:02:43)
[INFO] AutoMutEv:Effect of mutation residue number 40 from chain A (leucine) into
methionine: Energy difference: -0.0967 kcal/mol, Difference in average
score from the base case: -0.0121 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 38 from chain A (valine) into methionine:
Energy difference: -1.0405 kcal/mol, Difference in average score from the
base case: -0.0296 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 38 from chain A (valine) into leucine:
Energy difference: -0.7459 kcal/mol, Difference in average score from the
base case: 0.0216 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 38 from chain A (valine) into threonine:
Energy difference: -0.2108 kcal/mol, Difference in average score from the
base case: -0.0600 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 39 from chain A (alanine) into glycine:
Energy difference: -0.0719 kcal/mol, Difference in average score from the
base case: -0.0041 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 39 from chain A (alanine) into proline:
Energy difference: 2.4961 kcal/mol, Difference in average score from the
base case: 0.0153 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 39 from chain A (alanine) into serine:
Energy difference: -0.0297 kcal/mol, Difference in average score from the
base case: 0.0105 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 26 from chain A (leucine) into
methionine: Energy difference: -0.0504 kcal/mol, Difference in average
score from the base case: -0.0093 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 12 from chain A (tyrosine) into
histidine: Energy difference: -0.0656 kcal/mol, Difference in average score
from the base case: -0.0705 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 12 from chain A (tyrosine) into cysteine:
Energy difference: 0.7762 kcal/mol, Difference in average score from the
base case: -0.0008 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 12 from chain A (tyrosine) into
tryptophan: Energy difference: 0.1179 kcal/mol, Difference in average score
from the base case: 0.0134 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 41 from chain A (glycine) into aspartic
acid: Energy difference: 2.8552 kcal/mol, Difference in average score from
the base case: -0.0316 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 41 from chain A (glycine) into glutamic
acid: Energy difference: 2.8829 kcal/mol, Difference in average score from
the base case: -0.0339 (00:03:07)
[INFO] AutoMutEv:Effect of mutation residue number 41 from chain A (glycine) into
asparagine: Energy difference: 2.1679 kcal/mol, Difference in average score
from the base case: -0.0109 (00:03:07)
[INFO] Main: Simulation completed successfully. (00:03:10)
|
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 |
|---|---|---|---|---|
| 3 | A | A | -0.9584 | |
| 4 | E | A | -2.3176 | |
| 5 | G | A | 0.0000 | |
| 6 | Y | A | 0.0000 | |
| 7 | Q | A | 0.0000 | |
| 8 | Y | A | 0.0000 | |
| 9 | R | A | -1.0033 | |
| 10 | A | A | 0.0000 | |
| 11 | L | A | 0.7033 | |
| 12 | Y | A | 1.1130 | |
| 13 | D | A | -1.1709 | |
| 14 | Y | A | -1.6257 | |
| 15 | K | A | -3.3235 | |
| 16 | K | A | -4.1252 | |
| 17 | E | A | -4.2925 | |
| 18 | R | A | -4.6359 | |
| 19 | E | A | -4.2347 | |
| 20 | E | A | -4.1069 | |
| 21 | D | A | 0.0000 | |
| 22 | I | A | 0.0000 | |
| 23 | D | A | -2.5108 | |
| 24 | L | A | 0.0000 | |
| 25 | H | A | -0.5277 | |
| 26 | L | A | 1.1903 | |
| 27 | G | A | 0.2909 | |
| 28 | D | A | 0.0000 | |
| 29 | I | A | -0.4699 | |
| 30 | L | A | 0.0000 | |
| 31 | T | A | -1.1999 | |
| 32 | V | A | 0.0000 | |
| 33 | N | A | -1.7619 | |
| 34 | K | A | -1.7602 | |
| 35 | G | A | -0.5627 | |
| 36 | S | A | -0.1191 | |
| 37 | L | A | 0.0000 | |
| 38 | V | A | 1.6219 | |
| 39 | A | A | 1.2923 | |
| 40 | L | A | 1.9880 | |
| 41 | G | A | 0.8081 | |
| 42 | F | A | 0.3983 | |
| 43 | S | A | -0.5808 | |
| 44 | D | A | -2.1456 | |
| 45 | G | A | -1.7325 | |
| 46 | Q | A | -2.2612 | |
| 47 | E | A | -2.0848 | |
| 48 | A | A | -1.9754 | |
| 49 | R | A | -3.4204 | |
| 50 | P | A | 0.0000 | |
| 51 | E | A | -3.1116 | |
| 52 | E | A | -3.1392 | |
| 53 | I | A | -1.4477 | |
| 54 | G | A | -0.9948 | |
| 55 | W | A | -0.0695 | |
| 56 | L | A | 0.0000 | |
| 57 | N | A | -1.0236 | |
| 58 | G | A | 0.0000 | |
| 59 | Y | A | -1.1329 | |
| 60 | N | A | 0.0000 | |
| 61 | E | A | -2.1373 | |
| 62 | T | A | -1.1457 | |
| 63 | T | A | -1.5016 | |
| 64 | G | A | -2.0246 | |
| 65 | E | A | -3.0269 | |
| 66 | R | A | -3.0705 | |
| 67 | G | A | 0.0000 | |
| 68 | D | A | -2.1208 | |
| 69 | F | A | 0.0000 | |
| 70 | P | A | 0.0000 | |
| 71 | G | A | 0.0000 | |
| 72 | T | A | -1.0319 | |
| 73 | Y | A | 0.0298 | |
| 74 | V | A | 0.0000 | |
| 75 | E | A | -2.0347 | |
| 76 | Y | A | -0.9824 | |
| 77 | I | A | 0.4803 | |
| 78 | G | A | -0.7390 | |
| 79 | R | A | -2.6146 | |
| 80 | K | A | -2.7440 | |
| 81 | K | A | -2.3907 | |
| 82 | I | A | -0.6727 | |
| 83 | S | A | -0.4567 | |
| 84 | P | A | -0.2212 | |
| 85 | P | A | -0.2969 |
Automated mutations analysis - evolutionary conserved mutations
In the automated mutations mode, the server selects aggregation prone resides
and each selected residue is mutated based off an evolutionary approach.
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 .
Mutant |
Energetic effect |
Score comparison |
|||
| VM38A | -1.0405 | -0.0296 | View | CSV | PDB |
| VT38A | -0.2108 | -0.06 | View | CSV | PDB |
| YH12A | -0.0656 | -0.0705 | View | CSV | PDB |
| LM40A | -0.0967 | -0.0121 | View | CSV | PDB |
| LM26A | -0.0504 | -0.0093 | View | CSV | PDB |
| AG39A | -0.0719 | -0.0041 | View | CSV | PDB |
| GE41A | 2.8829 | -0.0339 | View | CSV | PDB |
| GD41A | 2.8552 | -0.0316 | View | CSV | PDB |
| YC12A | 0.7762 | -0.0008 | View | CSV | PDB |
| AS39A | -0.0297 | 0.0105 | 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