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
Shift List: Selects which shift list is the source of chemical shift information to make the residue type prediction
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) |
Remove From Spin System: Remove the selected resonance from the current spin system
Deassign Residue Type: Remove residue type information from the current spin system
Resonance Info: Show a table of information for the selected resonance, including a list of all peak dimension positions
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 |
Assign Spin System Type: Assign the residue type of the current spin system to the kind selected in the lower table
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