Spin System Type Scores

Predict Residue Type for a Spin System of Resonances

This tool aims to predict the residue type of a spin system based upon the chemical shifts of the resonances that it contains. The general principle is that different kinds of atoms in different kinds of residues have different observed distributions of chemical shifts. This system uses chemical shift distributions from the RefDB database, or otherwise from the BMRB where data is not available in RefDB. The observed chemical shifts of a spin system are compared to the per-atom distributions for each residue type and the residue types with the best matches are deemed to be more likely.

This system can work with various levels of information, although the more information the better. Naturally, the more chemical shifts you have in a spin system then the better the prediction of type, and 13C resonances are more distinctive than 1H on the whole. Also, setting the atom type of a resonance can have a big influence on the type of residue predicted, for example knowing that a 13C resonance at 63 ppm is of type CB points very strongly toward the residue being a serine. Atom type information can come from two sources: from a specific type assignment made by the user (via this popup or elsewhere) or by virtue of assignment in an experimental dimension that detects a restricted class of atom - e.g. 13C resonances in an HNCA experiment, assuming their shift matches, are of CA type as far as this prediction is concerned. Resonances that do not have a known atom type are compared with all of the unallocated types to find the combination that is most likely.

The residue type prediction is based on the list of resonances displayed in the upper table. Here the user can see the chemical shifts (from the selected shift list) and any specific atom type setting. The user may set the atom type for any of the resonances, which would normally be done to reduce prediction ambiguity, by double-clicking in the “Atom Type” column.

The lower table shows a ranked list of the probable residue types. All probability scores are normalised and represented as a percentage of the total of all scores, considering residue types in the selected chain. The type of a spin system may be set by clicking on a row of the lower table (hopefully a unique and high-scoring option) and then selecting [Assign Spin System Type]. If the user attempts to change the type of a spin system that is currently assigned to a specific residue then there is an opportunity to back out of the assignment, but otherwise any sequence specific information will be removed.

Caveats & Tips

It is assumed that the spectra from which the chemical shifts are derived are fairly well referenced.

A type prediction will always be given, no matter how few resonances are present in a spin system. This system says which of the available types are most likely, not how reliable the prediction is; the latter depends largely on the amount of information present. The user should not for example make a judgement based only on amide resonances. Reliability scores will be added in the future.

Rouge resonances in a spin system often adversely affect the prediction, if something is not genuinely in the spin system it should be removed.

The system will never predict the residue type to be something that does not appear in the selected molecular chain. Thus, make sure the chain selection is appropriate for your prediction.

Reference

The residue type prediction method is not published independently but is very similar to the Bayesian method presented in: Marin A, Malliavin TE, Nicolas P, Delsuc MA. From NMR chemical shifts to amino acid types: investigation of the predictive power carried by nuclei. J Biomol NMR. 2004 Sep;30(1):47-60.

One major difference however is that probabilities for resonances not being observed are not used. The CCPN prediction method is not only for complete spin systems and may be used at any time during the assignment process; here missing resonances are mostly due to the current assignment state and not such a useful indicator of residue type.

Main Panel

pulldown Shift List: Selects which shift list is the source of chemical shift information to make the residue type prediction

pulldown Chain: Selects which molecular chain the prediction is for; sets prior probabilities for the various residue types

Resonances

Table 1
Isotope The nuclear isotope type of the resonance within the current spin system
Name The assignment annotation for the spin system resonance within the current spin system
Shift Value The chemical shift of the resonance in the stated shift list
Shift Error The weighted standard deviation of the resonance chemical shift
Atom Type The current atom type of the resonance; when set this helps refine residue type prediction (Editable)

button Remove From Spin System: Remove the selected resonance from the current spin system

button Deassign Residue Type: Remove residue type information from the current spin system

button Resonance Info: Show a table of information for the selected resonance, including a list of all peak dimension positions

button Show Peaks: Show a table of the peaks to which the selected resonance is assigned

Type Scores

Table 2
Rank The ranking of the residue type possibility for the current spin system
Ccp Code The CCPN residue code for the type
% Probability The estimated percentage probability of the spin system being the residue type

button Assign Spin System Type: Assign the residue type of the current spin system to the kind selected in the lower table

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

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