| Chain sequence(s) |
A: QVQLVESGGGLVQPGGSLRLSCAASGGSEYSYSTFSLGWFRQAPGQGLEAVAAIASMGGLTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAAVRGYFMRLPSSHNFRYWGQGTLVTVS
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 minimization (00:00:01)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:00:55)
[INFO] AutoMutEv:Residue number 123 from chain A and a score of 1.621 (leucine) selected for
automated mutation (00:00:55)
[INFO] AutoMutEv:Residue number 11 from chain A and a score of 1.363 (leucine) selected for
automated mutation (00:00:55)
[INFO] AutoMutEv:Residue number 57 from chain A and a score of 1.063 omitted from automated
mutation (excluded by the user). (00:00:55)
[INFO] AutoMutEv:Residue number 105 from chain A and a score of 0.953 omitted from automated
mutation (excluded by the user). (00:00:55)
[INFO] AutoMutEv:Residue number 60 from chain A and a score of 0.878 omitted from automated
mutation (excluded by the user). (00:00:55)
[INFO] AutoMutEv:Residue number 10 from chain A and a score of 0.853 (glycine) selected for
automated mutation (00:00:55)
[INFO] AutoMutEv:Residue number 96 from chain A and a score of 0.795 (valine) selected for
automated mutation (00:00:55)
[INFO] AutoMutEv:Residue number 5 from chain A and a score of 0.682 (valine) selected for
automated mutation (00:00:55)
[INFO] AutoMutEv:Residue number 107 from chain A and a score of 0.671 omitted from automated
mutation (excluded by the user). (00:00:55)
[INFO] AutoMutEv:Residue number 122 from chain A and a score of 0.525 (threonine) selected
for automated mutation (00:00:55)
[INFO] AutoMutEv:Mutating residue number 123 from chain A (leucine) into methionine (00:00:55)
[INFO] AutoMutEv:Mutating residue number 10 from chain A (glycine) into glutamic acid (00:00:55)
[INFO] AutoMutEv:Mutating residue number 10 from chain A (glycine) into asparagine (00:00:55)
[INFO] AutoMutEv:Mutating residue number 10 from chain A (glycine) into aspartic acid (00:00:59)
[INFO] AutoMutEv:Mutating residue number 96 from chain A (valine) into threonine (00:01:00)
[INFO] AutoMutEv:Mutating residue number 11 from chain A (leucine) into methionine (00:01:01)
[INFO] AutoMutEv:Mutating residue number 96 from chain A (valine) into alanine (00:01:04)
[INFO] AutoMutEv:Mutating residue number 5 from chain A (valine) into threonine (00:01:04)
[INFO] AutoMutEv:Mutating residue number 5 from chain A (valine) into methionine (00:01:06)
[INFO] AutoMutEv:Mutating residue number 5 from chain A (valine) into alanine (00:01:08)
[INFO] AutoMutEv:Mutating residue number 96 from chain A (valine) into methionine (00:01:09)
[INFO] AutoMutEv:Mutating residue number 122 from chain A (threonine) into glutamic acid (00:01:11)
[INFO] AutoMutEv:Mutating residue number 122 from chain A (threonine) into aspartic acid (00:01:12)
[INFO] AutoMutEv:Mutating residue number 122 from chain A (threonine) into lysine (00:01:16)
[INFO] AutoMutEv:Effect of mutation residue number 123 from chain A (leucine) into
methionine: Energy difference: -0.4695 kcal/mol, Difference in average
score from the base case: -0.0304 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 11 from chain A (leucine) into
methionine: Energy difference: 0.0063 kcal/mol, Difference in average score
from the base case: -0.0138 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into glutamic
acid: Energy difference: 2.5060 kcal/mol, Difference in average score from
the base case: -0.0428 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into aspartic
acid: Energy difference: 2.1582 kcal/mol, Difference in average score from
the base case: -0.0420 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 10 from chain A (glycine) into
asparagine: Energy difference: 1.5002 kcal/mol, Difference in average score
from the base case: -0.0263 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 96 from chain A (valine) into threonine:
Energy difference: 0.6135 kcal/mol, Difference in average score from the
base case: -0.0122 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 96 from chain A (valine) into alanine:
Energy difference: 1.4705 kcal/mol, Difference in average score from the
base case: -0.0119 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 96 from chain A (valine) into methionine:
Energy difference: -0.0454 kcal/mol, Difference in average score from the
base case: -0.0095 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into threonine:
Energy difference: 0.2584 kcal/mol, Difference in average score from the
base case: -0.0361 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into alanine:
Energy difference: 0.9309 kcal/mol, Difference in average score from the
base case: -0.0435 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 5 from chain A (valine) into methionine:
Energy difference: -0.0729 kcal/mol, Difference in average score from the
base case: -0.0266 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 122 from chain A (threonine) into
glutamic acid: Energy difference: 1.5264 kcal/mol, Difference in average
score from the base case: -0.0181 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 122 from chain A (threonine) into
aspartic acid: Energy difference: 1.0949 kcal/mol, Difference in average
score from the base case: -0.0103 (00:01:21)
[INFO] AutoMutEv:Effect of mutation residue number 122 from chain A (threonine) into lysine:
Energy difference: 0.7501 kcal/mol, Difference in average score from the
base case: -0.0219 (00:01:21)
[INFO] Main: Simulation completed successfully. (00:01:25)
|
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 | Q | A | -1.5509 | |
| 2 | V | A | -1.3151 | |
| 3 | Q | A | -1.3700 | |
| 4 | L | A | 0.0000 | |
| 5 | V | A | 0.6817 | |
| 6 | E | A | 0.0000 | |
| 7 | S | A | -0.3384 | |
| 8 | G | A | -0.7355 | |
| 9 | G | A | 0.0637 | |
| 10 | G | A | 0.8532 | |
| 11 | L | A | 1.3626 | |
| 12 | V | A | -0.0461 | |
| 13 | Q | A | -1.2938 | |
| 14 | P | A | -1.6163 | |
| 15 | G | A | -1.4049 | |
| 16 | G | A | -1.1086 | |
| 17 | S | A | -1.3363 | |
| 18 | L | A | -1.1632 | |
| 19 | R | A | -2.3599 | |
| 20 | L | A | 0.0000 | |
| 21 | S | A | -0.6255 | |
| 22 | C | A | 0.0000 | |
| 23 | A | A | -0.3122 | |
| 24 | A | A | -0.5603 | |
| 25 | S | A | -1.0336 | |
| 26 | G | A | -1.4112 | |
| 27 | G | A | -1.3441 | |
| 28 | S | A | -1.2529 | |
| 29 | E | A | -1.7761 | |
| 30 | Y | A | -0.8986 | |
| 31 | S | A | -0.7556 | |
| 32 | Y | A | -1.0925 | |
| 33 | S | A | -0.6025 | |
| 34 | T | A | -0.1473 | |
| 35 | F | A | 0.0000 | |
| 36 | S | A | 0.0000 | |
| 37 | L | A | 0.0000 | |
| 38 | G | A | 0.0000 | |
| 39 | W | A | 0.0000 | |
| 40 | F | A | 0.0000 | |
| 41 | R | A | 0.0000 | |
| 42 | Q | A | -0.7684 | |
| 43 | A | A | -1.0534 | |
| 44 | P | A | -1.1205 | |
| 45 | G | A | -1.3585 | |
| 46 | Q | A | -1.8422 | |
| 47 | G | A | -1.2170 | |
| 48 | L | A | -0.3346 | |
| 49 | E | A | -0.9751 | |
| 50 | A | A | -0.4663 | |
| 51 | V | A | 0.0000 | |
| 52 | A | A | 0.0000 | |
| 53 | A | A | 0.0000 | |
| 54 | I | A | 0.0000 | |
| 55 | A | A | 0.0000 | |
| 56 | S | A | 0.0000 | |
| 57 | M | A | 1.0633 | |
| 58 | G | A | 0.3341 | |
| 59 | G | A | 0.3134 | |
| 60 | L | A | 0.8778 | |
| 61 | T | A | 0.2856 | |
| 62 | Y | A | -0.2454 | |
| 63 | Y | A | -1.0164 | |
| 64 | A | A | -1.3783 | |
| 65 | D | A | -2.3548 | |
| 66 | S | A | -1.8397 | |
| 67 | V | A | 0.0000 | |
| 68 | K | A | -2.5215 | |
| 69 | G | A | -1.7288 | |
| 70 | R | A | -1.4050 | |
| 71 | F | A | 0.0000 | |
| 72 | T | A | -1.0139 | |
| 73 | I | A | 0.0000 | |
| 74 | S | A | -0.6492 | |
| 75 | R | A | -1.2981 | |
| 76 | D | A | -1.9306 | |
| 77 | N | A | -2.1689 | |
| 78 | S | A | -1.8441 | |
| 79 | K | A | -2.5929 | |
| 80 | N | A | -2.0200 | |
| 81 | T | A | 0.0000 | |
| 82 | L | A | 0.0000 | |
| 83 | Y | A | 0.0000 | |
| 84 | L | A | 0.0000 | |
| 85 | Q | A | -1.7566 | |
| 86 | M | A | 0.0000 | |
| 87 | N | A | -1.4644 | |
| 88 | S | A | -1.1722 | |
| 89 | L | A | 0.0000 | |
| 90 | R | A | -2.3135 | |
| 91 | A | A | -1.7308 | |
| 92 | E | A | -2.2803 | |
| 93 | D | A | 0.0000 | |
| 94 | T | A | -0.4502 | |
| 95 | A | A | 0.0000 | |
| 96 | V | A | 0.7949 | |
| 97 | Y | A | 0.0000 | |
| 98 | Y | A | 0.3102 | |
| 99 | C | A | 0.0000 | |
| 100 | A | A | 0.0000 | |
| 101 | A | A | 0.0000 | |
| 102 | V | A | -1.2383 | |
| 103 | R | A | -1.9150 | |
| 104 | G | A | -0.6120 | |
| 105 | Y | A | 0.9529 | |
| 106 | F | A | 0.0000 | |
| 107 | M | A | 0.6713 | |
| 108 | R | A | -0.8652 | |
| 109 | L | A | -0.5289 | |
| 110 | P | A | 0.0000 | |
| 111 | S | A | -0.8768 | |
| 112 | S | A | -1.0196 | |
| 113 | H | A | -1.7074 | |
| 114 | N | A | -1.6108 | |
| 115 | F | A | 0.0000 | |
| 116 | R | A | -2.3281 | |
| 117 | Y | A | 0.0000 | |
| 118 | W | A | -0.3187 | |
| 119 | G | A | -0.2497 | |
| 120 | Q | A | -0.9414 | |
| 121 | G | A | 0.0157 | |
| 122 | T | A | 0.5248 | |
| 123 | L | A | 1.6205 | |
| 124 | V | A | 0.0000 | |
| 125 | T | A | 0.3702 | |
| 126 | V | A | 0.0000 | |
| 127 | S | A | -0.5764 |
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 |
|||
| LM123A | -0.4695 | -0.0304 | View | CSV | PDB |
| VM5A | -0.0729 | -0.0266 | View | CSV | PDB |
| VM96A | -0.0454 | -0.0095 | View | CSV | PDB |
| LM11A | 0.0063 | -0.0138 | View | CSV | PDB |
| VT5A | 0.2584 | -0.0361 | View | CSV | PDB |
| TK122A | 0.7501 | -0.0219 | View | CSV | PDB |
| VT96A | 0.6135 | -0.0122 | View | CSV | PDB |
| GD10A | 2.1582 | -0.042 | View | CSV | PDB |
| GN10A | 1.5002 | -0.0263 | View | CSV | PDB |
| TE122A | 1.5264 | -0.0181 | 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