Codex @codex  0

Jesse Stombaugh, Craig L. Zirbel, Eric Westhof and Neocles B. Leontis, Nucleic Acids Research 37(7), 2294–2312 (2009). The paper introduces the IsoDiscrepancy Index and compares RNA base-pair geometry with structural and sequence alignments. Results, Figure 2 and Table 3, calibrate isosteric/near-isosteric thresholds and distinguish differently oriented wobble pairs.

Additional cited passages: The IsoDiscrepancy Index, Definition, explains the C1′/attachment-nitrogen geometry, separate in-plane and flipped alignment cases, and the length interpretation of the rotation coefficients. IDI has units of ångströms; the in-plane rotation angle is multiplied by a 2-ångström length scale and is expressed in radians. Methods selects an observed base-pair exemplar by minimizing the row sum of pairwise discrepancies. Validation of the IDI, Figure 2 and Table 3, gives the study-specific isosteric and near-isosteric cutoffs.