How to run AmyloidMutants?
To use the webserver in its simplest form, the
Basic Input tab needs only the following inputs:
- Paste your amino acid sequence into the top box.
- Choose a schema; this defines the abstract amyloid shape you'd like to fold
- Optionally mutate select residues; enter the sequence position in the left box,
and select what residues that position can have via pull-down menus.
- Enter your email address (optional).
- Submit your request by clicking on the "Submit" button!
How to interpret results?
Please see our Examples page for a
description of the output the AmyloidMutants webserver generates.
How to speed computation?
High-accuracy AmyloidMutants can take a while. Please contact
you are interested in having longer jobs run or for other collaborations.
Depending on choice of schema and sequence length, speed improvments
may be seen by increasing the Threshold,
turning off Allow kinks, or reducing the Number of samples
What if my browser doesn't render the page?
AmyloidMutants was designed using newer web standards and thus we suggest using
Mozilla Firefox 3.5, Internet Explorer 8, Safari 5, or newer to view
the best user interface.
Earlier browsers should be automatically detected and redirected to
a Simplified Interface that will work on
If your using one of the suggested browsers and still having problems, make
amyloid.csail.mit.edu cookie to reset your state to begin again.
We also appreciate any feedback on any problems via the
firstname.lastname@example.org email address.
Optional parameters in the Landscape Parameters tab:
The Landscape Parameters tab allows one to modify the
structural schema parameters and energetic parameters to account
only for folds which match a specific ranges of constraints.
Modification of these constraints can effect runtime greatly.
The first six parameters define limits on permissible amyloid shapes:
Three other parameters also control what landscape is computed
dependent on energy:
- β-strands: The minimum and maximum number of residues within
- N-term coil: The minimum and maximum number of residues which can
be assigned as disordered coil at the N-terminus of the sequence
- C-term coil: The minimum and maximum number of residues which can
be assigned as disordered coil at the C-terminus of the sequence
- Inner coil: The minimum and maximum length of a coil region
within the amyloid structure (minimum length of 1).
- Serpentine slip: Applicable to the serpentine schema only.
The permitted difference in β-sheet/strand length between adjacent,
packed β-sheets in a cross-pleated fold.
- Allow kinks: Applicable to the β-solenoid schemas only.
This indicates if the ensemble analysis allows one "kink" in the
standard β-sheet in/out orientation per β-sheet.
- Threshold: This option improves computation time by only
allowing amyloid structures that are comprised of the top N% of
β-strands/β-strand interactions, energetically.
Enter a number between 0.0 and 1.0, where 0.90 means that only the top
10% of β-strands/β-strand interactions are included
in the computation.
- Coil bias: This allows one to investigate which
This applies a bias to the energy function to either favor the formation
of β-sheet (numbers between 0.0 and 1.0) or of coil (high numbers).
The bias acts as a multiplier, so the value 0.125 is 8x more likely to
form β-sheet, and the value 8.0 is 8x more likely to form
coil. Amongst other things, this allows one to investigate which
β-strands/β-strand interactions or coil regions are most
energetically favorable without thresholding.
- Energy function: This chooses which energy function is used.
Optional parameters in the Sampling tab:
The AmyloidMutants webserver computes an amyloid
sequence/structure landscape and samples a population of
sequences and their complete fibril conformation.
After sampling, a clustering algorithm is run and results
are generated from these clusters (see Examples).
The Sampling tab contains options controlling
the details of this sampling.
Note, one can perform a new clustering analysis on the samples
generated from a past computation via the
Rerun Clustering input form above.
- Number of samples: The number of samples to collect.
- Number of clusters: The number of clusters to generate via
Partition-Around-Mediods (PAM) clustering.
- Unique Sampling: Ensure that every sample is unique
- Boltzmann sampling factor: Only applicable to if Unique Sampling
is enabled. This terminates sampling when the set of unique samples' energetic
weights exceeds N% of the entire ensemble.
This value ranges from 0.0 to 1.0.
For example, assigning a value of 0.99 would terminate sampling
when 99% of the weighted ensemble has been accounted for (or when
the Number of samples limit is reached, whichever comes first).
- Random seed: Enter a random seed for deterministic sampling.
A value of 0 indicates no random seed
- Distance metric: This determines what distance metric to
use during clustering. For example to separate the samples by sequence,
identifying what structures are found in common sequence mutants, choose "Sequence-only."
To separate samples by structure, identifying what mutations are found
in common structures, choose "Structure."
- PAM clustering method: Internal algorithmic option for PAM clustering
Optional parameters in the Advanced Mutations tab:
The Advanced Mutations tab allows one to specify
many more mutation sites and mutation types than permitted in
the Basic Input tab.
To specify a mutation protocol, please enter above a list of declarations
(one per line) that can be of the following form:
- 13 -> APZ
Residue position 13 permits an Ala(A), Pro(P), or the original residue
in the sequence(Z). Note: if Z is not specified, the original residue will
not be included as a possibility.
- 13-15 -> APZ
Residues 13, 14, and 15 all permit Ala(A), Pro(P) or the original residue
in the sequence(Z).
- V -> AP
All Val(V) residues in the original sequence will be changed to permit
either Ala(A) or Pro(P) (and not Val(V)).
- 14=A 15=V
These two lines declare that residue position 14 will be Ala(A) and 15 will be Val(V)
or position 14 will be Thr(T) and 15 will be Pro(P) (2 possible permutations).
Multiple definitions like this permit specific correlated mutations
(i.e. the declaration "14->AT", and "15->VP" would permit 4 permutations instead of 2).