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

pulldown Chain: Selects which molecular chain the spin system residue types will be predicted for; determines which range of types are available

pulldown Shift List: Selects which shift list will be used as the source of chemical shift information to make the residue type predictions

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Options

check Keep existing types?: Whether any existing residue type information should be preserved, when predicting the type of others

float -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

int 20: The number of best scoring residue type mappings, from the Monte Carlo search, to use un the prediction

int 100000: The number of iterative steps that will be used in the Monte Carlo search of best spin system to residue type mappings

selector *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

button Run Typing: Execute the Monte Carlo search that will make the residue type predictions for the spin systems

button Assign Types: Assign the residue type of spin systems with a unique type prediction and prediction score above the stated threshold

button 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

button Show Peaks: Show a table of peaks that are assigned to the resonances of the selected spin system

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