Assignment : Spin System Typing
Predict Which Types of Residue Spin Systems Represent
This popup window uses chemical shift information, obtained from the
resonances of a spin system group, to predict which kind of residue a spin
system could be. Naturally, the more resonances/shifts there are in a spin
system the better the prediction will be. Predictions are either made for a
single spin system in isolation, or for a whole chain; by shuffling the
residue to spin system mapping to give the optimum arrangement. Prediction for
individual spin systems, as accessed by [Show Individual Classification], is
covered in the Spin System Type Scores popup and will not be discussed
here.
Finding the Optimal Arrangement of Residue Types
This system attempts to find the best match of spin system to residue type by
performing a Monte Carlo search to arrange each group of chemical shifts
amongst the residue types found in the chain. The main principle is that the
chain’s residues dictate how many spin systems of a given type may be found,
such that for example if there is only one Threonine residue then only one
spin system may be predicted to be of Threonine type. This result comes
naturally from shuffling the spin systems, with their chemical shifts, amongst
the residue slots (disregarding sequence position).
The prediction is made my selecting the chain and shift list to use, then
which kinds of isotope to consider, by toggling the relevant buttons, choosing
various Monte Carlo search options and finally selecting [Run Typing]. The
prediction may take some time to run, depending upon the number of residues
and spin systems that are being matched, but gives a graphical output of the
progress. If the final prediction looks good the “Highest Scoring Mappings”
display may be closed and [Assign Types] may be used to set the residue types
for all of the spin systems in the main table that match only a single type
and have a score above the assignment threshold value. Spin systems that
already have a type or full residue assignment will not be affected.
The default Monte Carlo search options ought to be appropriate for a small
protein (100 residues) with 1H and 13C chemical shift information. Increasing
the number of search steps may help if the search does not converge; still
swaps between optimal assignments toward the end of the search. Increasing the
ensemble size (how many test mappings are optimised at the same time) may help
if the prediction gets stuck in local minima; different runs predict different
arrangement, but larger ensembles require more search steps to converge. Where
a spin system has multiple residue types predicted these are the types that
come out of the final ensemble for that set of shifts, i.e. at this point the
ensemble of solutions differ.
Overall, it should be noted that if a human being cannot readily predict the
probably types of a spin system from its shifts alone, then this search tool
cannot be expected to do a good job; it is merely an optimiser to address the
problem of shuffling spin systems within a chain.
The scores are currently unnormalised log-odds values and are not especially
meaningful in the human sense, other than higher is better (closer to zero
for negative values). This issue will be addressed in the future.
Spin systems without a unique type prediction will not get a final score.
Main Panel
Chain: Selects which molecular chain the spin system residue types will be predicted for; determines which range of types are available
Shift List: Selects which shift list will be used as the source of chemical shift information to make the residue type predictions
Clone: Clone popup window
Help: Show popup help document
Close: Close popup
Options
Keep existing types?: Whether any existing residue type information should be preserved, when predicting the type of others
-20.0: The lower limit for the predicted residue type to be set with “Assign Types”; needs to be adjusted according to result statistics and amount of shift data
20: The number of best scoring residue type mappings, from the Monte Carlo search, to use un the prediction
100000: The number of iterative steps that will be used in the Monte Carlo search of best spin system to residue type mappings
*None*: Selects which kinds of resonances, in terms of isotope, the residue type predictions will be made with
Spin Systems
Table 1 |
# |
The spin system serial number |
Residue |
The residue to which the spin system may currently be assigned |
Use? |
Set whether to include a particular spin system in the type predictions (Editable) |
Score |
The spin system to residue type match score for a prediction; higher (less negative) is better |
Types |
The predicted types of residue that the spin system may be |
Shifts |
The chemical shifts in the spin system that will be used in the analysis |
Run Typing: Execute the Monte Carlo search that will make the residue type predictions for the spin systems
Assign Types: Assign the residue type of spin systems with a unique type prediction and prediction score above the stated threshold
Show Individual Classification: Show a residue type prediction for the selected spin system alone; only considers that spin system of shifts, not how all spin systems fit to the sequence
Show Peaks: Show a table of peaks that are assigned to the resonances of the selected spin system