AmyloidMutants

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 amyloid@csail.mit.edu if 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 (see below).

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 all browsers. If your using one of the suggested browsers and still having problems, make sure that javascript and cookies are enabled, and delete the amyloid.csail.mit.edu cookie to reset your state to begin again. We also appreciate any feedback on any problems via the amyloid@csail.mit.edu 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:

  • β-strands: The minimum and maximum number of residues within any β-strand.
  • 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.
Three other parameters also control what landscape is computed dependent on energy:
  • 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.

  • 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
Note, one can perform a new clustering analysis on the samples generated from a past computation via the Rerun Clustering input form above.



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
    14=T 15=P
    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).