Hi Mike,

Thanks for posting on the 3DNA Forum. I sort of understand of your point, but I do not think there exists a table of "local base pair parameters and/or simple base pair parameters for the pairs in the

**twelve families of Leontis-Westhof base pairs**". The LW notation of 12 base-pair classes is intuitive in concept, qualitative in nature, and incomplete in practice.

For example, have a close look at the "

**1MSY** FR3D basepairs pairwise interaction annotations" compiled by the Leontis-Zirbel group. Can you figure out what

`ncWW` and

`ntSH` in the following two entries mean?

`1MSY|1|A|U|2647 ncWW 1MSY|1|A|G|2673`

1MSY|1|A|U|2653 ntSH 1MSY|1|A|C|2667

As another example, the Watson-Crick (WC) and the G–U wobble pairs all belong to the cWW class. Nevertheless, WC and wobble pairs are obviously different. Moreover, and the G–U and U–G wobble pairs are also dissimilar above the base-pair level. See the recent review article "

The multiple flavors of GoU pairs in RNA" by Westhof

*et al*. in which the LW notation is not mentioned at all. Also, there are more variants of G∙U pairs than those wobble-like "GoU pairs" mentioned in the Westhof review.

For a comprehensive, and quantitative classification of base pairs in DNA or RNA, please see our recent article "

Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G∙ A Pairs". See also read the section "3.2.2 Base pairs" in the

DSSR User Manual.

HTH,

Xiang-Jun