| Base pair classification (under construction) |
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Currently, there are at least two accepted classification of base pairing patterns. The first one uses a simple denomination based on the H-bonds that are formed in each pairing. W. Saenger [1] originally used this denomination for pairings involving two or more H-bonds. D. Gautheret et al. [2] later added pairings involving only one H-bonds. The RNA modeling software Mc-Sym currently uses this classification. The second classification, or geometry based nomenclature, comes from N.B. Leontis & E. Westhof [3] and employs a naming scheme based on the chemical "faces" involved in the pairings as well as on the relative orientation of the sugar to ribose bonds. Unfortunately, none of these representations captures all the information needed to establish a one-to-one correspondence between a particular pairing and the associated name. The advantages and disavdvantages of each representation are indicated below. As a part of the elaboration of the Madison format for secondary structure, we wish to design a new classification that will uniquely represent each type of pairing interaction and let a user be as specific as wanted when naming a pairing. The set of pages on the left contains all identified base pairings, as well as the corresponding names and number of occurrences in the PDB structures. Isosteric pairs are computed using the distance metric described in [4] using a distance cutoff of 1.5 Å. Characteristics of the MC-SYM nomenclature:
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