The RNA IsoDiscrepancy Index, abbreviated IDI, is a numerical measure of how two base pairs differ in the geometry relevant to their attached backbones. Lower values indicate closer RNA base-pair isostericity. Jesse Stombaugh, Craig L. Zirbel, Eric Westhof and Neocles B. Leontis introduced it to make comparisons more quantitative than assigning pairs only to broad geometric families.[ref]
Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others. The IsoDiscrepancy Index, Definition
The comparison considers the separation of the ribose atoms and the relative positions and orientations of the bases at their glycosidic bonds. The attachment nitrogen is N1 for a pyrimidine and N9 for a purine. Thus matching the distance between two sugar attachment points alone does not establish matching base orientation. The published construction handles in-plane alignment and comparisons requiring an out-of-plane flip separately.[ref]
Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others. Definition, geometric criteria and Cases 1–2
IDI has units of ångströms, not a dimensionless probability scale. In the in-plane case, the method weights an orientation angle by a 2-ångström length scale. An original illustration of that rotation term isThis is one weighted rotation contribution, not the complete IDI formula. Translation, separation and the paired orientation comparisons also matter. Expressing an angle in radians is essential to this length interpretation.[ref]
Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others. Definition, interpretation of the coefficient multiplying the in-plane rotation angle
The authors calibrated their classification using structural distributions: IDI at most 2.0 ångströms is isosteric, above 2.0 through 3.3 ångströms is near-isosteric, and larger values are more dissimilar. These are the study's method-specific cutoffs. A chosen score of 1.8 therefore falls in its first category, whereas 2.6 falls in its second; neither is an energy or a probability.[ref]
Frequency and isostericity of RNA base pairs by Jesse Stombaugh and others. Validation of the IDI, Figure 2 and Table 3
Interchanging the two structures being compared leaves the discrepancy unchanged; reversing the nucleotide order within only one base pair is a different operation. An RNA isostericity matrix can display such comparisons, but sequence context and model quality still affect interpretation. A geometrically plausible substitution is a structural hypothesis, not a guarantee of unchanged folding stability or molecular recognition.
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